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(-) Description

Title :  UCH-L5 IN COMPLEX WITH UBIQUITIN-PROPARGYL BOUND TO THE RPN13 DEUBAD DOMAIN
 
Authors :  D. D. Sahtoe, W. J. Van Dijk, F. El Oualid, R. Ekkebus, H. Ovaa, T. K. Six
Date :  18 Dec 14  (Deposition) - 04 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydrolase, Deubiquitinating Enzyme, Dub, Uch37, Uchl5, Proteasome, Adrm1, Rpn13, Deubad, Uch, Ubiquitin-Propargyl (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. D. Sahtoe, W. J. Van Dijk, F. El Oualid, R. Ekkebus, H. Ovaa, T. K. Sixma
Mechanism Of Uch-L5 Activation And Inhibition By Deubad Domains In Rpn13 And Ino80G.
Mol. Cell V. 57 887 2015
PubMed-ID: 25702870  |  Reference-DOI: 10.1016/J.MOLCEL.2014.12.039

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
    Chains: A
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-NKI-3C-LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: ACTIVE SITE CYS88 COVALENTLY LINKED TO UBIQUITIN-PROPARGYL
    Synonym: UCH-L5, UBIQUITIN C-TERMINAL HYDROLASE UCH37, UBIQUITIN THIOESTERASE L5
    Variant: ISOFORM 3
 
Molecule 2 - POLYUBIQUITIN-B
    Chains: B
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: GLY76 OF UBIQUITIN IS REPLACED BY GLY-AYE THAT IS COVALENTLY LINKED TO THE ACTIVE SITE CYS88 OF UCH-L5
    Synonym: UBIQUITIN
    Synthetic: YES
 
Molecule 3 - PROTEASOMAL UBIQUITIN RECEPTOR ADRM1
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDF-NKI-HIS-3C-LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector Type: PLASMID
    Fragment: DEUBAD DOMAIN, RESIDUES 266-388
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RPN13,110 KDA CELL MEMBRANE GLYCOPROTEIN, GP110, ADHESION-REGULATING MOLECULE 1, ARM-1, PROTEASOME REGULATORY PARTICLE NON-ATPASE 13, HRPN13, RPN13 HOMOLOG

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1AYE1Mod. Amino AcidPROP-2-EN-1-AMINE

(-) Sites  (0, 0)

(no "Site" information available for 4UEL)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UEL)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:47 -Pro A:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UEL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UEL)

(-) Exons   (0, 0)

(no "Exon" information available for 4UEL)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhhhhhhhhhh...eeeeee....hhhhhh...eeeeeeeee.........ee..hhhhhh..........hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..............eeeeeeeee..eeeee.......eeeee.....hhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uel A   6 GEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEENSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQN 320
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       161       171       181       191       201       211       221       231       241   ||  258       268       278       288       298       308       318  
                                                                                                                                                                             153|                                                                                  245|                                                                   
                                                                                                                                                                              160                                                                                   253                                                                   


Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4uel B   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGx  76
                                    10        20        30        40        50        60        70     |
                                                                                                      76-AYE


Chain C from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4uel C 287 DLASVLTPEIMAPILANADVQERLLPYLPSGESLPQTADEIQNTLTSPQFQQALGMFSAALASGQLGPLMCQFGLPAEAVEAANKGDVEAFAKAMQNN 384
                                   296       306       316       326       336       346       356       366       376
   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 4UEL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UEL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UEL)

(-) Gene Ontology  (118, 130)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Lys A:47 - Pro A:48   [ RasMol ]  
 

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  4uel
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  UCHL5_HUMAN | Q9Y5K5
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 Related Entries

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

UniProtKB/Swiss-Prot
        ADRM1_HUMAN | Q16186: 2kqz 2kr0 2l5v 2mkz 2nbk 2nbv 4uem 4wlq 4wlr 5irs 5v1y 5v1z
        UBB_HUMAN | P0CG47: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1yx5 1yx6 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2hth 2ibi 2j7q 2jf5 2jzz 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2l0f 2l0t 2mbb 2mro 2msg 2n13 2nr2 2o6v 2ojr 2pe9 2pea 2w9n 2wdt 2xew 2xk5 2y5b 2zcb 3a33 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3oj3 3oj4 3ons 3phd 3ptf 3zlz 3znh 4uf6 4whv 4wlr 4wur 4wzp 4xof 4zfr 4zft 4zpz 4zux 5bnb 5caw 5cra 5cvm 5cvn 5cvo 5d0k 5d0m 5dfl 5dk8 5e6j 5edv 5emz 5eya 5gjq 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5ibk 5ifr 5j8p 5jbv 5jby 5jg6 5jp3 5jtj 5jtv 5k9p 5kgf 5khy 5l8h 5l8w 5l9t 5ln1 5lrv 5lrw 5lrx 5m93 5mnj 5n2w 5n38 5nl5 5nlj 5nvg 5tof 5tog 5ulf 5ulh 5ulk 5v1y 5v1z 5vey 5vf0 5w46 5x3m 5x3n 5x3o 5xbo 5xdp 5xk4 5xk5
        UCHL5_HUMAN | Q9Y5K5: 3a7s 3ihr 3rii 3ris 3tb3 4uem 4uf5 4uf6 4wlp

(-) Related Entries Specified in the PDB File

4uem UCH-L5 IN COMPLEX WITH THE RPN13 DEUBAD DOMAIN