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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UAF1/USP12 COMPLEX IN F222 SPACE GROUP
 
Authors :  H. Li, A. D. D'Andrea, N. Zheng
Date :  18 May 16  (Deposition) - 20 Jul 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Wd40 Domain, Sumo-Like Domain, Ubiquitin-Specific Protease 12, Usp12, Usp1-Associated Factor 1, Deubiquitinating Enzyme, Dub, Protein Binding-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Li, K. S. Lim, H. Kim, T. R. Hinds, U. Jo, H. Mao, C. E. Weller, J. Sun, C. Chatterjee, A. D. D'Andrea, N. Zheng
Allosteric Activation Of Ubiquitin-Specific Proteases By Beta-Propeller Proteins Uaf1 And Wdr20.
Mol. Cell V. 63 249 2016
PubMed-ID: 27373336  |  Reference-DOI: 10.1016/J.MOLCEL.2016.05.031

(-) Compounds

Molecule 1 - WD REPEAT-CONTAINING PROTEIN 48
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Gene: WDR48, KIAA1449, UAF1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: USP1-ASSOCIATED FACTOR 1,WD REPEAT ENDOSOMAL PROTEIN,P80
 
Molecule 2 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 12
    Chains: A
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Gene: USP12, UBH1, USP12L1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEUBIQUITINATING ENZYME 12,UBIQUITIN THIOESTERASE 12, UBIQUITIN-HYDROLYZING ENZYME 1,UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:186 , CYS A:189 , CYS A:233 , CYS A:236binding site for residue ZN A 401

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:233 -A:236

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K1B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K1B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K1B)

(-) Exons   (0, 0)

(no "Exon" information available for 5K1B)

(-) 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:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhh........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeeee.....eeeeeeee.eeee...hhhhhhh....eee.....eee....eee.eeeeeeeee...eeeeee...........eeee...eeeeeeeeeeee.......ee.eee....eeee..eeee.....hhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k1b A  40 GLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQESLLTCLADLFHSIATQVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEEPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVSITHCLRGFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFSYRVVFPLELRLFPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHWLLFDDDIVEKIDAQAIEEFYKNSESGYILFYQSRD 370
                                    49        59        69   ||   83        93||     108       118       128       138    || 173       183       193       203  ||   217       227       237       247       257    || 279       297       307       317       329       339       356       366    
                                                            73|              94|                                        143|                                  206|                                                262|         287|                          325|                 348|              
                                                             78              100                                         169                                   211                                                 275          296                           328                  356              


Chain B from PDB  Type:PROTEIN  Length:579
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...........eeeeeee....eeeeee...eeeeee..........eeee.....eeeeeee....eeeeee....eeeee....eeeeee......eeeeeee....eeeeee....eeeeehhhhh...........eee......eeeeee......eeeee......ee......eee..........eeee.....eeeee.....eeeee.hhheeee........eeeeee.....eeeeee......eee...............eeeeee........eeeeee....eeeee.........eee.....eee..ee....eeeeee....eeeee....eeeee....hhhhhh............eee.....eeeee........eee.hhhh.......eeehhhhhhhhhh..hhhhh..................eeeeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee....eeeeee...hhhhhhhhhhhh.hhhhhhh.eee..ee.....hhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k1b B  12 RRKVQVSYVIRDEVEKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKQDPYIASMEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGFCMSTLRTHKDYVKALAYAKDKELVASAGLDRQIFLWDVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGHTDNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQRCIATYRVHDEGVWALQVNDAFTHVYSGGRDRKIYCTDLRPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKWTLTPLCTQPDQVIKGGASIIQCHILNDKRHILTKDTNNNVAYWDVLKACKVEDLGKVDFEDEIKKFKMVYVPNWFSVDLKTGMLTITLDESDCFAAWVSAKDAGFSSPSDPKLNLGGLLLQALLEYWPRTHVNPMVQKGNGYFQVPPHTPVIFGEAGRTLFRLLCRDSGGETESMLLNETVPQWVIDITVDKNMPKFNKIPFYLQPKKDRLSASDMLQVRKVMEHVYEKAVLAEEKIELLCQDQVLDPNMDLRTVKHFIWDLTLHYR 673
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281||     292       302       312       322   ||  352       362       372       382       392       402      |413       423       433       443       453|      465       475      |502       512       523       533       543       553       563       582       592       602||     640       650       660 ||      
                                                                                                                                                                                                                                                                                                        282|                                       326|                                                           409|                                       453|                       482|                 520|                                              571|                   603|                           662|      
                                                                                                                                                                                                                                                                                                         284                                        347                                                            411                                        456                        500                  522                                               581                    632                            667
   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 5K1B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K1B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K1B)

(-) Gene Ontology  (30, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBP12_HUMAN | O75317: 5k16 5k1a 5k1c 5l8w
        WDR48_HUMAN | Q8TAF3: 5cvl 5cvn 5cvo 5k1a 5k1c 5l8e 5l8w

(-) Related Entries Specified in the PDB File

5k16 5k19 5k1a 5k1c