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(-) Description

Title :  INSIGHTS INTO THE MECHANISM OF DEUBIQUITINATION BY JAMM DEUBIQUITINASES FROM CO-CRYSTAL STRUCTURES OF ENZYME WITH SUBSTRATE AND PRODUCT
 
Authors :  R. K. Shrestha, J. A. Ronau, C. Das
Date :  04 Mar 14  (Deposition) - 18 Jun 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Helix-Beta-Helix Sandwich, Ubiquitin, Deubiquitination, Zinc Metalloprotease, Lysine 63-Linked Polyubiquitin, Hydrolase- Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Shrestha, J. A. Ronau, C. W. Davies, R. G. Guenette, E. R. Strieter L. N. Paul, C. Das
Insights Into The Mechanism Of Deubiquitination By Jamm Deubiquitinases From Cocrystal Structures Of The Enzyme Wit The Substrate And Product.
Biochemistry V. 53 3199 2014
PubMed-ID: 24787148  |  Reference-DOI: 10.1021/BI5003162

(-) Compounds

Molecule 1 - AMSH-LIKE PROTEASE SST2
    Chains: A
    EC Number: 3.4.19.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6-P1
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN UNP RESIDUES 245-435
    Gene: SPAC19B12.10, SST2
    Mutation: YES
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
    Synonym: SUPPRESSOR OF STE12 DELETION PROTEIN 2
 
Molecule 2 - PROTEIN UBBP4
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 77-152
    Gene: UBBP4, UBIQUITIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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
1EDO3Ligand/Ion1,2-ETHANEDIOL
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:356 , CYS A:397 , HIS A:404 , HIS A:406BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREGLN A:416 , PRO A:417 , GLY A:418 , HOH A:608BINDING SITE FOR RESIDUE EDO A 503
3AC3SOFTWAREHOH A:612 , THR B:7 , LEU B:8 , LEU B:69 , VAL B:70 , LEU B:71 , HOH B:207BINDING SITE FOR RESIDUE EDO B 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:387 -Pro A:388
2Gln A:416 -Pro A:417

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PQT)

(-) 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:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....ee.eeeeehhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..eee....eee.hhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeee....eeeeeee..hhhhhhhhhh.............eee......eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pqt A 249 KIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVALHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLR 433
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428     


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................eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4pqt B   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70
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  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 4PQT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

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    Asp A:387 - Pro A:388   [ RasMol ]  
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  4pqt
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  SST2_SCHPO | Q9P371
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  3.4.19.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        SST2_SCHPO | Q9P371: 4jxe 4k1r 4ms7 4msd 4msj 4msm 4msq 4nql 4zd4 4zd5 4zfr 4zft

(-) Related Entries Specified in the PDB File

2znv AMSH-LP E292A BOUND TO LYS63-LINKED UBIQUITIN DIMER
4k1r CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE SST2 CATALYTIC DOMAIN AND UBIQUITIN