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(-) Description

Title :  CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE SST2 CATALYTIC DOMAIN
 
Authors :  R. K. Shrestha, C. Das
Date :  28 Mar 13  (Deposition) - 30 Apr 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Helix-Beta-Helix Sandwich, Ubiquitin, Dequbiquitination, Zinc Metalloprotease, Deubiquitination, Cytosol, Hydrolase (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, B
    EC Number: 3.4.19.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (245-435)
    Gene: SST2, SPAC19B12.10
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
    Synonym: SUPPRESSOR OF STE12 DELETION PROTEIN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:341 , HIS A:343 , ASP A:354 , HOH A:634BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREHIS A:356 , CYS A:397 , HIS A:404 , HIS A:406BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREGLY A:318 , THR A:319 , TYR A:361BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWARELYS A:426 , LEU A:427BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWAREHIS B:341 , HIS B:343 , ASP B:354 , HOH B:636BINDING SITE FOR RESIDUE ZN B 501
06AC6SOFTWAREHIS B:356 , CYS B:397 , HIS B:404 , HIS B:406BINDING SITE FOR RESIDUE ZN B 502
07AC7SOFTWAREPHE B:403 , HIS B:404 , HOH B:635 , HOH B:674BINDING SITE FOR RESIDUE EDO B 503
08AC8SOFTWAREVAL B:429 , VAL B:430 , ASP B:431BINDING SITE FOR RESIDUE EDO B 504
09AC9SOFTWAREGLU B:255 , LEU B:386 , PRO B:388 , GLU B:389BINDING SITE FOR RESIDUE EDO B 505
10BC1SOFTWARECYS B:288 , CYS B:317 , GLY B:318 , THR B:319 , TYR B:361BINDING SITE FOR RESIDUE EDO B 506
11BC2SOFTWARELYS B:249 , ARG B:261 , THR B:262 , ASN B:298 , HOH B:631BINDING SITE FOR RESIDUE TRS B 507
12BC3SOFTWAREHIS B:304 , HIS B:332 , GLN B:428BINDING SITE FOR RESIDUE TRS B 508

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:387 -Pro A:388
2Gln A:416 -Pro A:417
3Asp B:387 -Pro B:388
4Gln B:416 -Pro B:417

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JXE)

(-) 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:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..............hhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeee....eeeeeee..hhhhhhhhhh.............eee......eeee....eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jxe A 247 TFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLRV 434
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426        


Chain B from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.....ee..eeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..............hhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeee....eeeeeee..hhhhhhhhhh.............eee......eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jxe B 248 FKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLR 433
                                   257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427
   Legend:   → Mismatch (orange background)
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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 4JXE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3rzu STRUCTURE OF CATALYTIC DOMAIN, HUMAN PROTEIN AMSH