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(-) Description

Title :  CRYSTAL STRUCTURE OF FREE UBIQUITIN-SPECIFIC PROTEASE 12
 
Authors :  H. Li, A. D. D'Andrea, N. Zheng
Date :  17 May 16  (Deposition) - 20 Jul 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Deubiquitination, Deubiquitnating Enzyme, Dub, Hydrolase (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 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 12
    Chains: A, B
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Fragment: RESIDUES 16-370
    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 Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:186 , CYS A:189 , CYS A:233 , CYS A:236binding site for residue ZN A 401
2AC2SOFTWAREILE A:192 , SER A:193 , SER A:194binding site for residue GOL A 402
3AC3SOFTWARECYS B:186 , CYS B:189 , CYS B:233 , CYS B:236binding site for residue ZN B 401
4AC4SOFTWAREILE B:107 , THR B:108 , ARG B:111binding site for residue GOL B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K16)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K16)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K16)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K16)

(-) Exons   (0, 0)

(no "Exon" information available for 5K16)

(-) Sequences/Alignments

Asymmetric 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:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhheeee..eee.........eeee..eee.....eehhhhhhhhh.....ee......ee.eee..eeee...eeeeee..eeee....eeee....ee...eeeee.........eeeeeeeeeeeeee.....eeeeeeeee..eeeeee..eeeeehhhhhhhhh......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k16 A  21 SALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQKKESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQEKQNPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQNTSITHCLRGFSNTETKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEKIDAQAIEEFYGLTSKNSESGYILFYQSRD 370
                                    30        40        50        60        70  ||    82        92       102       112       122       132       142       168       178       188       198       208       218     ||233       243       253       263       273       283       293       303       313       323       333       343       356       366    
                                                                               73|                                                                       150|                                                      224|                                                                                                                       352|              
                                                                                76                                                                        167                                                       230                                                                                                                        356              


Chain B from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeeee.....eeeeeeee..eeee.....hhhhhhh............eeee....eeeeeeeeeeeee...eeeeeee.eeee....eeee.........eeeee.........eeeeeeeeeeeeee......eeeeeeee..eeeeee..eeeeehhhhhhhhh....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k16 B  19 NASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQEKQPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQNTSITHCLRGFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEKIDAQAIEEFYGLKNSESGYILFYQSRD 370
                                    28        38        48        58        68        78        88        98       108       118       128       138       148||     177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  ||   362        
                                                                                                                                                            149|                                                                                                                                                                                  350|              
                                                                                                                                                             169                                                                                                                                                                                   356
   Legend:   → Mismatch (orange background)
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  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 5K16)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K16)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K16)

(-) Gene Ontology  (11, 11)

Asymmetric 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: 5k1a 5k1b 5k1c 5l8w

(-) Related Entries Specified in the PDB File

5k19 5k1a 5k1b 5k1c