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(-) Description

Title :  STRUCTURE OF THE D1D2 DOMAIN OF USP4, THE CONSERVED CATALYTIC DOMAIN
 
Authors :  M. P. A. Luna-Vargas, A. C. Faesen, W. J. Van Dijk, M. Rape, A. Fish, T. K.
Date :  20 Jan 11  (Deposition) - 06 Apr 11  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Clerici, M. P. A. Luna-Vargas, A. C. Faesen, T. K. Sixma
The Dusp-Ubl Domain Of Usp4 Enhances Its Catalytic Efficiency By Promoting Ubiquitin Exchange.
Nat. Commun. V. 5 5399 2014
PubMed-ID: 25404403  |  Reference-DOI: 10.1038/NCOMMS6399

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4
    Chains: A, B, C, D, E, F
    EC Number: 3.1.2.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-NKI-B3C/LIC AND PET46-EK/LIC
    Expression System Strain: ROSETTA2(DE3) PLYSS-T1R
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 296-490,765-932
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 4, DEUBIQUITINATING ENZYME 4, UBIQUITIN THIOLESTERASE 4, UBIQUITOUS NUCLEAR PROTEIN HOMOLOG, USP4

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1CME6Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2SO42Ligand/IonSULFATE ION
3ZN6Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:461 , CYS A:464 , CYS A:799 , CYS A:802BINDING SITE FOR RESIDUE ZN A1000
2AC2SOFTWAREGLN A:391 , MET A:877 , GLY A:878 , HOH A:2248 , HOH A:2249 , ARG B:373 , LYS C:348 , ARG C:381BINDING SITE FOR RESIDUE SO4 A1926
3AC3SOFTWARECYS B:461 , CYS B:464 , CYS B:799 , CYS B:802BINDING SITE FOR RESIDUE ZN B1000
4AC4SOFTWARECYS C:461 , CYS C:464 , CYS C:799 , CYS C:802BINDING SITE FOR RESIDUE ZN C1000
5AC5SOFTWARETYR C:476 , THR C:478BINDING SITE FOR RESIDUE SO4 C1925
6AC6SOFTWARECYS D:461 , CYS D:464 , CYS D:799 , CYS D:802BINDING SITE FOR RESIDUE ZN D1000
7AC7SOFTWARECYS E:461 , CYS E:464BINDING SITE FOR RESIDUE ZN E1000
8AC8SOFTWARECYS F:461 , CYS F:464BINDING SITE FOR RESIDUE ZN F1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y6E)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu B:793 -His B:794

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y6E)

(-) PROSITE Motifs  (3, 18)

Asymmetric/Biological Unit (3, 18)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1USP_3PS50235 Ubiquitin specific protease (USP) domain profile.UBP4_HUMAN302-923
 
 
 
 
 		  6A:302-923
B:302-923
C:302-923
D:302-923
E:302-923
F:302-923
2USP_1PS00972 Ubiquitin specific protease (USP) domain signature 1.UBP4_HUMAN303-318
 
 
 
 
 		  6A:303-318
B:303-318
C:303-318
D:303-318
E:303-318
F:303-318
3USP_2PS00973 Ubiquitin specific protease (USP) domain signature 2.UBP4_HUMAN865-882
 
 
 
 
 		  6A:865-882
B:865-882
C:865-882
D:865-882
E:865-882
F:865-882

(-) Exons   (0, 0)

(no "Exon" information available for 2Y6E)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:337
 aligned with UBP4_HUMAN | Q13107 from UniProtKB/Swiss-Prot  Length:963

    Alignment length:629
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916         
           UBP4_HUMAN   297 IQPGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEVFLVPADPHCRPTQYRVTVPLMGAVSDLCEALSRLSGIAAENMVVADVYNHRFHKIFQMDEGLNHIMPRDDIFVYEVCSTSVDGSECVTLPVYFRERKSRPSSTSSASALYGQPLLLSVPKHKLTLESLYQAVCDRISRYVKQPLPDEFGSSPLEPGACNGSRNSCEGEDEEEMEHQEEGKEQLSETEGSGEDEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSYGTADINSLAADGKLLKLNSRSTLAMDWDSETRRLYYDEQESEAYEKHVSMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDD 925
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.........hhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeee......eeeeeeee..eeee...---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.eehhhhhhhhh..ee...-..eee....eee..eeeeeeee...eeeeeee.eee....eee....ee.....ee.hhh.........eeeeeeeeeee......eeeeeee......eeeee..eeee.hhhhh....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----USP_3  PDB: A:302-923 UniProt: 302-923                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        -- PROSITE (1)
                PROSITE (2) ------USP_1           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------USP_2             ------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6e A 297 IQPGLCGLGNLGNTcFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TVALRDCIELFTTMETLGE-DPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDD 925
                                   306    |  316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476      |  -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       776       786      |796       806       816       826       836       846       856       866       876       886       896       906       916         
                                        311-CME                                                                                                                                                                     483                                                                                                                                                                                                                                                                                                 775               793 |                                                                                                                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            795                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:339
 aligned with UBP4_HUMAN | Q13107 from UniProtKB/Swiss-Prot  Length:963

    Alignment length:635
                                   305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925     
           UBP4_HUMAN   296 HIQPGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEVFLVPADPHCRPTQYRVTVPLMGAVSDLCEALSRLSGIAAENMVVADVYNHRFHKIFQMDEGLNHIMPRDDIFVYEVCSTSVDGSECVTLPVYFRERKSRPSSTSSASALYGQPLLLSVPKHKLTLESLYQAVCDRISRYVKQPLPDEFGSSPLEPGACNGSRNSCEGEDEEEMEHQEEGKEQLSETEGSGEDEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSYGTADINSLAADGKLLKLNSRSTLAMDWDSETRRLYYDEQESEAYEKHVSMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDEFYKT 930
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......-----.....hhhhhhhhhhhhhhh...hhhhhhhheeeeeeee......eeeeeeee..eeee...---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.eehhhhhhhhhh.ee......eee....eee..eeeeeeee...eeeeeee.eee....eee....ee.....ee.hhh.........eeeeeeeeeee......eeeeeee......eeeee..eeee.hhhhh....eeeeeeee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------USP_3  PDB: B:302-923 UniProt: 302-923                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ------- PROSITE (1)
                PROSITE (2) -------USP_1           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------USP_2             ------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6e B 296 HIQPGLCGLGNLGNTcFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKP-----DANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDEFYKT 930
                                   305     | 315       325       335       345       355       365       375       385       395       405       415|     |425       435       445       455       465       475       | -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925     
                                         311-CME                                                                                                  416   422                                                          483                                                                                                                                                                                                                                                                                                 775                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:331
 aligned with UBP4_HUMAN | Q13107 from UniProtKB/Swiss-Prot  Length:963

    Alignment length:629
                                   305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915         
           UBP4_HUMAN   296 HIQPGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEVFLVPADPHCRPTQYRVTVPLMGAVSDLCEALSRLSGIAAENMVVADVYNHRFHKIFQMDEGLNHIMPRDDIFVYEVCSTSVDGSECVTLPVYFRERKSRPSSTSSASALYGQPLLLSVPKHKLTLESLYQAVCDRISRYVKQPLPDEFGSSPLEPGACNGSRNSCEGEDEEEMEHQEEGKEQLSETEGSGEDEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSYGTADINSLAADGKLLKLNSRSTLAMDWDSETRRLYYDEQESEAYEKHVSMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRD 924
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.........hhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........----.....hhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeee......eeeeeeee..eeee...--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..eehhhhhhhhhh.ee.----.ee......ee..eeeeeeee...eeeeeee.eee....eee....ee.....ee.hhh.........eeeeeeeeeee......eeeeeee......eeeee..eeee.hhhhh....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------USP_3  PDB: C:302-923 UniProt: 302-923                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) -------USP_1           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------USP_2             ------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6e C 296 HIQPGLCGLGNLGNTcFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPY----DANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPL--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTVALRDCIELFTTMETL----PWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRD 924
                                   305     | 315       325       335       345       355       365       375       385       395       405       415 |    |425       435       445       455       465       475       | -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       775       785     |   -|      805       815       825       835       845       855       865       875       885       895       905       915         
                                         311-CME                                                                                                   417  422                                                          483                                                                                                                                                                                                                                                                                                774              791  796                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:328
 aligned with UBP4_HUMAN | Q13107 from UniProtKB/Swiss-Prot  Length:963

    Alignment length:631
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926 
           UBP4_HUMAN   297 IQPGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEVFLVPADPHCRPTQYRVTVPLMGAVSDLCEALSRLSGIAAENMVVADVYNHRFHKIFQMDEGLNHIMPRDDIFVYEVCSTSVDGSECVTLPVYFRERKSRPSSTSSASALYGQPLLLSVPKHKLTLESLYQAVCDRISRYVKQPLPDEFGSSPLEPGACNGSRNSCEGEDEEEMEHQEEGKEQLSETEGSGEDEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSYGTADINSLAADGKLLKLNSRSTLAMDWDSETRRLYYDEQESEAYEKHVSMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDEF 927
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.........hhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........-----....hhhhhhhhhhhhhhhhh.hhhhhhhheeeeeee......-.eeeeeee..eee....--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.eeehhhhhhhhhh.ee.-----.........--.eeeeeeee...eeeeee..eee....eee...eee.....ee.hhh.........eeeeeeeeeee......eeeeeee......eeeee..eeee.hhhhh....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----USP_3  PDB: D:302-923 UniProt: 302-923                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ---- PROSITE (1)
                PROSITE (2) ------USP_1           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------USP_2             --------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6e D 297 IQPGLCGLGNLGNTcFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPY-----ANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECA-VSVTFDPFCYLTLPLPL--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTVALRDCIELFTTMETL-----WYCPNCKKH--ATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDEF 927
                                   306    |  316       326       336       346       356       366       376       386       396       406       416|     |426       436       446       456        |-|      476      |  -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       776       786    |    -|       |- |     816       826       836       846       856       866       876       886       896       906       916       926 
                                        311-CME                                                                                                   417   423                                       465 |             483                                                                                                                                                                                                                                                                                                774              791   797     805  |                                                                                                                       
                                                                                                                                                                                                    467                                                                                                                                                                                                                                                                                                                                                  808                                                                                                                       


Chain E from PDB  Type:PROTEIN  Length:319
 aligned with UBP4_HUMAN | Q13107 from UniProtKB/Swiss-Prot  Length:963

    Alignment length:633
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926   
           UBP4_HUMAN   297 IQPGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEVFLVPADPHCRPTQYRVTVPLMGAVSDLCEALSRLSGIAAENMVVADVYNHRFHKIFQMDEGLNHIMPRDDIFVYEVCSTSVDGSECVTLPVYFRERKSRPSSTSSASALYGQPLLLSVPKHKLTLESLYQAVCDRISRYVKQPLPDEFGSSPLEPGACNGSRNSCEGEDEEEMEHQEEGKEQLSETEGSGEDEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSYGTADINSLAADGKLLKLNSRSTLAMDWDSETRRLYYDEQESEAYEKHVSMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDEFYK 929
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.........hhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........-------..hhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeee......eeeeeeee..eeee...---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.eehhhhhhhhhh..----------------...eeeeeeee...eeeeeee.eee....eee....ee.....ee.hhh.........eeeeeeeeeee......eeeeeee......eeeee..eeee.hhhhh....eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----USP_3  PDB: E:302-923 UniProt: 302-923                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ------ PROSITE (1)
                PROSITE (2) ------USP_1           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------USP_2             ----------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6e E 297 IQPGLCGLGNLGNTcFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPY-------GRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TVALRDCIELFTTME----------------QQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDEFYK 929
                                   306    |  316       326       336       346       356       366       376       386       396       406       416|      426       436       446       456       466       476      |  -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       776       786  |      -       806       816       826       836       846       856       866       876       886       896       906       916       926   
                                        311-CME                                                                                                   417     425                                                       483                                                                                                                                                                                                                                                                                                 775           789              806                                                                                                                           


Chain F from PDB  Type:PROTEIN  Length:323
 aligned with UBP4_HUMAN | Q13107 from UniProtKB/Swiss-Prot  Length:963

    Alignment length:631
                                   305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925 
           UBP4_HUMAN   296 HIQPGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEVFLVPADPHCRPTQYRVTVPLMGAVSDLCEALSRLSGIAAENMVVADVYNHRFHKIFQMDEGLNHIMPRDDIFVYEVCSTSVDGSECVTLPVYFRERKSRPSSTSSASALYGQPLLLSVPKHKLTLESLYQAVCDRISRYVKQPLPDEFGSSPLEPGACNGSRNSCEGEDEEEMEHQEEGKEQLSETEGSGEDEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSYGTADINSLAADGKLLKLNSRSTLAMDWDSETRRLYYDEQESEAYEKHVSMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDE 926
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---UCH-2y6eF01 F:299-920                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ------ Pfam domains (1)
           Pfam domains (2) ---UCH-2y6eF02 F:299-920                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ------ Pfam domains (2)
           Pfam domains (3) ---UCH-2y6eF03 F:299-920                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ------ Pfam domains (3)
           Pfam domains (4) ---UCH-2y6eF04 F:299-920                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ------ Pfam domains (4)
           Pfam domains (5) ---UCH-2y6eF05 F:299-920                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ------ Pfam domains (5)
           Pfam domains (6) ---UCH-2y6eF06 F:299-920                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ------ Pfam domains (6)
         Sec.struct. author .......ee.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.........hhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......---.......hhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeee......eeeeeeee..eeee....--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.eehhhhhhhhhh....---------------..eeeeeeee...eeeeeee.eee....eee....ee.....ee.............eeeeeeeeeee......eeeeeee......eeeee..eeee.hhhhh....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------USP_3  PDB: F:302-923 UniProt: 302-923                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        --- PROSITE (1)
                PROSITE (2) -------USP_1           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------USP_2             -------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6e F 296 HIQPGLCGLGNLGNTcFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKP---LKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLK--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TVALRDCIELFTTMETL---------------QATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDE 926
                                   305     | 315       325       335       345       355       365       375       385       395       405       415|   |  425       435       445       455       465       475        |-         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       775       785     |   -         - |     815       825       835       845       855       865       875       885       895       905       915       925 
                                         311-CME                                                                                                  416 420                                                             484                                                                                                                                                                                                                                                                                                775             791             807
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2Y6E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y6E)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_CA (169)
(-)
Family: UCH (11)
(-)
Homo sapiens (Human) (6)
1aUCH-2y6eF01F:299-920
1bUCH-2y6eF02F:299-920
1cUCH-2y6eF03F:299-920
1dUCH-2y6eF04F:299-920
1eUCH-2y6eF05F:299-920
1fUCH-2y6eF06F:299-920

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (UBP4_HUMAN | Q13107)
molecular function
    GO:0031685    adenosine receptor binding    Interacting selectively and non-covalently with an adenosine receptor.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004843    thiol-dependent ubiquitin-specific protease activity    Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
biological process
    GO:0031397    negative regulation of protein ubiquitination    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:0034394    protein localization to cell surface    A process in which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0031647    regulation of protein stability    Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
    GO:0000244    spliceosomal tri-snRNP complex assembly    The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        UBP4_HUMAN | Q13107: 5ctr

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