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(-) Description

Title :  CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE SST2 CATALYTIC DOMAIN
 
Authors :  R. K. Shrestha, J. A. Ronau, C. Das
Date :  18 Sep 13  (Deposition) - 18 Jun 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Helix-Beta-Helix Sandwich, Ubiquitin, Dequbiquitination, Zinc Metalloprotease, 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: 511693
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 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, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:341 , HIS A:343 , ASP A:354 , HOH A:713BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREHIS A:356 , CYS A:397 , HIS A:404 , HIS A:406BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWARETHR A:254 , HOH A:602BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWAREGLU A:286 , THR A:316 , CYS A:317 , VAL A:353 , ASP A:354 , THR A:357 , HOH A:713BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWARECYS A:317 , GLY A:318 , THR A:319 , TYR A:361BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWAREPHE A:403 , HIS A:404 , HOH A:616BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWARELYS A:249 , HIS A:251 , ARG A:261 , THR A:262 , ASN A:298 , HOH A:613 , HOH A:637 , HOH A:659BINDING SITE FOR RESIDUE TRS A 507
08AC8SOFTWAREHIS B:356 , CYS B:397 , HIS B:404 , HIS B:406BINDING SITE FOR RESIDUE ZN B 501
09AC9SOFTWAREHIS B:341 , HIS B:343 , ASP B:354 , HOH B:715BINDING SITE FOR RESIDUE ZN B 502
10BC1SOFTWAREGLU B:286 , THR B:316 , CYS B:317 , TRP B:339 , VAL B:353 , ASP B:354 , THR B:357 , HOH B:715BINDING SITE FOR RESIDUE EDO B 503
11BC2SOFTWAREGLY B:318 , THR B:319 , TYR B:361BINDING SITE FOR RESIDUE EDO B 504

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:288 -A:317
2B:288 -B:317

(-) 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 4MS7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MS7)

(-) Exons   (0, 0)

(no "Exon" information available for 4MS7)

(-) 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:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.....ee..eeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..eee....eee.hhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeeehhhheeeeeee..hhhhhhhhhh.............eee......eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ms7 A 248 FKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLR 433
                                   257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427      


Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....ee..eeee.hhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeeee..eee....eee.hhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeee....eeeeeee..hhhhhhhhhh.............eee......eeee....eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ms7 B 247 TFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLRV 434
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426
   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 4MS7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MS7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MS7)

(-) Gene Ontology  (14, 14)

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  Cis Peptide Bonds
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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 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
4jxe STRUCTURE OF CATALYTIC DOMAIN, S.POMBE SSTE
4msd CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEIN SST2 T319I MUTANT
4msj CRYSTAL STRUCTURE OF S. POMBE AMSH-LIKE PROTEASE SST2 CATALYTIC DOMAIN FROM P212121 SPACE GROUP
4msm CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEASE SST2 E286A MUTANT BOUND TO UBIQUITIN
4msq CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEASE SST2 CATALYTIC DOMAIN BOUND TO UBIQUITIN