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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ALKALINE FORM OF V8 PROTEASE FROM STAPHYLOCOCCUS AUREUS
 
Authors :  K. Yamada, M. Ohta, T. Hasegawa, K. Torii, M. Murakami, K. Kouyama
Date :  10 May 04  (Deposition) - 01 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Glutamyl Endopeptidase, Virulence Factor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yamada, M. Ohta, T. Hasegawa, K. Torii, M. Murakami, K. Kouyama
Crystal Structure Of An Alkaline Form Of V8 Protease From Staphylococcus Aureus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMYL ENDOPEPTIDASE
    Chains: A
    EC Number: 3.4.21.19
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: V8
    Synonym: V8 PROTEASE, STAPHYLOCOCCAL SERINE PROTEINASE, V8 PROTEINASE, ENDOPROTEINASE GLU-C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

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
1AC1SOFTWAREASP A:7 , HIS A:9 , HIS A:107 , LYS A:147BINDING SITE FOR RESIDUE ZN A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WCZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WCZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WCZ)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1V8_HISPS00672 Serine proteases, V8 family, histidine active site.SSPA_STAA8105-119  1A:37-51
SSPA_STAAU105-119  1A:37-51
2V8_SERPS00673 Serine proteases, V8 family, serine active site.SSPA_STAA8232-242  1A:164-174
SSPA_STAAU232-242  1A:164-174

(-) Exons   (0, 0)

(no "Exon" information available for 1WCZ)

(-) 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:215
 aligned with SSPA_STAA8 | Q2FZL2 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:216
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      
           SSPA_STAA8    69 VILPNNDRHQITDTTNGHYAPVTYIQVEAPTGTFIASGVVVGKDTLLTNKHVVDATHGDPHALKAFPSAINQDNYPNGGFTAEQITKYSGEGDLAIVKFSPNEQNKHIGEVVKPATMSNNAETQVNQNITVTGYPGDKPVATMWESKGKITYLKGEAMQYDLSTTGGNSGSPVFNEKNEVIGIHWGGVPNEFNGAVFINENVRNFLKQNIEDIHFA 284
               SCOP domains d1wcza_ A: V8 protease                                                                                                                                                                                                   SCOP domains
               CATH domains 1wczA01       1wczA02 A:15-11 5 Trypsin-like serine proteases                                                      1wczA01 A:1-14,A:116-216 Trypsin-like serine proteases                                                CATH domains
               Pfam domains -----------------------------------Trypsin_2-1wczA01 A:36-183                                                                                                                          --------------------------------- Pfam domains
         Sec.struct. author ......eeeee....hhhhh.eeeeeee.-..eeeeeeee....eeeehhhhhhhhh.hhh.eeeee............eeeeeeee.......eeeee.......hhhhhh...............eeeeee.........eeeeeeeeeeee..eeee...........eee.....eeeeeeeee...eeeeee.hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------V8_HIS         ----------------------------------------------------------------------------------------------------------------V8_SER     ------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wcz A   1 VILPNNDRHQITDTTNGHYAPVTYIQVEA-TGTFIASGVVVGKDTLLTNKHVVDATHGDPHALKAFPSAINQDNYPNGGFTAEQITKYSGEGDLAIVKFSPNEQNKHIGEVVKPATMSNNAETQVNQNITVTGYPGDKPVATMWESKGKITYLKGEAMQYDLSTTGGNSGSPVFNEKNEVIGIHWGGVPNEFNGAVFINENVRNFLKQNIEDINFA 216
                                    10        20        |-|       40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
                                                       29 |                                                                                                                                                                                         
                                                         31                                                                                                                                                                                         


Chain A from PDB  Type:PROTEIN  Length:215
 aligned with SSPA_STAAU | P0C1U8 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:216
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      
           SSPA_STAAU    69 VILPNNDRHQITDTTNGHYAPVTYIQVEAPTGTFIASGVVVGKDTLLTNKHVVDATHGDPHALKAFPSAINQDNYPNGGFTAEQITKYSGEGDLAIVKFSPNEQNKHIGEVVKPATMSNNAETQVNQNITVTGYPGDKPVATMWESKGKITYLKGEAMQYDLSTTGGNSGSPVFNEKNEVIGIHWGGVPNEFNGAVFINENVRNFLKQNIEDIHFA 284
               SCOP domains d1wcza_ A: V8 protease                                                                                                                                                                                                   SCOP domains
               CATH domains 1wczA01       1wczA02 A:15-11 5 Trypsin-like serine proteases                                                      1wczA01 A:1-14,A:116-216 Trypsin-like serine proteases                                                CATH domains
               Pfam domains -----------------------------------Trypsin_2-1wczA01 A:36-183                                                                                                                          --------------------------------- Pfam domains
         Sec.struct. author ......eeeee....hhhhh.eeeeeee.-..eeeeeeee....eeeehhhhhhhhh.hhh.eeeee............eeeeeeee.......eeeee.......hhhhhh...............eeeeee.........eeeeeeeeeeee..eeee...........eee.....eeeeeeeee...eeeeee.hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------V8_HIS         ----------------------------------------------------------------------------------------------------------------V8_SER     ------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wcz A   1 VILPNNDRHQITDTTNGHYAPVTYIQVEA-TGTFIASGVVVGKDTLLTNKHVVDATHGDPHALKAFPSAINQDNYPNGGFTAEQITKYSGEGDLAIVKFSPNEQNKHIGEVVKPATMSNNAETQVNQNITVTGYPGDKPVATMWESKGKITYLKGEAMQYDLSTTGGNSGSPVFNEKNEVIGIHWGGVPNEFNGAVFINENVRNFLKQNIEDINFA 216
                                    10        20        |-|       40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
                                                       29 |                                                                                                                                                                                         
                                                         31
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (7, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SSPA_STAA8 | Q2FZL2)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A   (SSPA_STAAU | P0C1U8)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1qy6 A PROTEASE BELONGING TO THE SAME PROTEIN FAMILY