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(-) Description

Title :  CRYSTAL STRUCTURE OF THE AUTOPROCESSED VIBRIOLYSIN MCP-02 WITH E369A MUTATION
 
Authors :  X. Gao, J. Wang, L. Chen, J. -W. Wu, Y. -Z. Zhang
Date :  30 Jun 10  (Deposition) - 06 Oct 10  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Autoprocessed Complex, Mcp-02, The Thermolysin Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Gao, J. Wang, D. -Q. Yu, F. Bian, B. -B. Xie, X. -L. Chen, B. -C. Zhou, L. -H. Lai, Z. -X. Wang, J. -W. Wu, Y. -Z. Zhang
Structural Basis For The Autoprocessing Of Zinc Metalloproteases In The Thermolysin Family
Proc. Natl. Acad. Sci. Usa V. 107 17569 2010
PubMed-ID: 20876133  |  Reference-DOI: 10.1073/PNAS.1005681107

(-) Compounds

Molecule 1 - SECRETED METALLOPROTEASE MCP02
    Chains: A
    EC Number: 3.4.24.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PROPEPTIDE DOMAIN, RESIDUES 25-204
    Organism Scientific: PSEUDOALTEROMONAS SP.
    Organism Taxid: 234831
    Other Details: PROPEPTIDE OF MCP02
    Strain: SM9913
    Synonym: MCP-02
 
Molecule 2 - SECRETED METALLOPROTEASE MCP02
    Chains: B
    EC Number: 3.4.24.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: THE CATALYTIC DOMAIN, RESIDUES 205-519
    Mutation: YES
    Organism Scientific: PSEUDOALTEROMONAS SP.
    Organism Taxid: 234831
    Strain: SM9913
    Synonym: MCP-02

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:204 , HIS B:345 , HIS B:349 , HIS B:428BINDING SITE FOR RESIDUE ZN B 1
2AC2SOFTWAREASP B:341 , GLU B:377 , GLU B:380 , ASP B:388 , LEU B:390 , HOH B:638BINDING SITE FOR RESIDUE CA B 520

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1B:237 -B:263
2B:482 -B:510

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly B:234 -Asn B:235
2Cys B:263 -Pro B:264
3Phe B:268 -Lys B:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NQZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NQZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3NQZ)

(-) 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:175
 aligned with A1DRD5_PSEU9 | A1DRD5 from UniProtKB/TrEMBL  Length:727

    Alignment length:180
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204
         A1DRD5_PSEU9    25 ANKKYLNQQPTINNMVQSNSASLLSVSPNQLIGLSVGNELVVLKEFTSNNGEVTRRYQQTYQGIPVIGDTVSLTFNNGMLKKAHGAAVYNIDEDLSDVSAKLTKKDAILKGSKTGIAAKSVGLKKHNEQSRLAIWVDDQNKAHLVYEVSYVTYGKSPSRPYLIIDANTGEVLLSYDNLQH 204
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------FTP-3nqzA02 A:63-112                              ------------PepSY-3nqzA01 A:125-199                                                    ----- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhh..-----..hhhhhhh....eeeeeeeeee....eeeeeeeeee..ee.....eeeeee..eeeeeeeeeeehhhhh........hhhhhhhhhh.hhhhhhhh....eeeeeeeeeee.....eeeeeeeeee........eeeeee.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nqz A  25 ANKKYLNQQPTINNMVQSN-----SVSPNQLIGLSVGNELVVLKEFTSNNGEVTRRYQQTYQGIPVIGDTVSLTFNNGMLKKAHGAAVYNIDEDLSDVSAKLTKKDAILKGSKTGIAAKSVGLKKHNEQSRLAIWVDDQNKAHLVYEVSYVTYGKSPSRPYLIIDANTGEVLLSYDNLQH 204
                                    34        |-    |   54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204
                                             43    49                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:307
 aligned with A1DRD5_PSEU9 | A1DRD5 from UniProtKB/TrEMBL  Length:727

    Alignment length:307
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       
         A1DRD5_PSEU9   205 ANATGPGGNLKTGKYLYGTDFDSLDVSQSGNTCSMNNANVRTINLNGGTSGSSAYSFTCPENTFKEINGAYSPLNDAHFFGNVIFNMYNDWLGTAPLSFQLQMRVHYSSNYENAFWDGSAMTFGDGQNTFYPLVSLDVSAHEVSHGFTEQNSGLIYNGKPGGLNEAFSDMAGEAAEFYMKGSNDWLVGKDIFKGNGALRYMNNPTQDGRSIDNQSNYYSGMDVHYSSGVYNKAFYNLATTPGWDTQKAFIVMARANQLYWSAGVGWDLAGNGVMDAACDLNYDPNDVKAALAAVGVNSNLSSGSDCA 511
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------Peptidase_M4-3nqzB01 B:211-354                                                                                                                  -Peptidase_M4_C-3nqzB02 B:356-500                                                                                                                 ----------- Pfam domains
         Sec.struct. author .ee.eeeee...eeeee......ee.eee..eee.....eeeee...........eee.............hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee......eee....eeee..........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh..........hhhhhh....hhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nqz B 205 ANATGPGGNLKTGKYLYGTDFDSLDVSQSGNTCSMNNANVRTINLNGGTSGSSAYSFTCPENTFKEINGAYSPLNDAHFFGNVIFNMYNDWLGTAPLSFQLQMRVHYSSNYENAFWDGSAMTFGDGQNTFYPLVSLDVSAHEVSHGFTEQNSGLIYNGKPGGLNAAFSDMAGEAAEFYMKGSNDWLVGKDIFKGNGALRYMNNPTQDGRSIDNQSNYYSGMDVHYSSGVYNKAFYNLATTPGWDTQKAFIVMARANQLYWSAGVGWDLAGNGVMDAACDLNYDPNDVKAALAAVGVNSNLSSGSDCA 511
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3NQZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NQZ)

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: PepSY (8)
(-)
Clan: Peptidase_MA (251)
(-)
Clan: no clan defined [family: FTP] (2)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A1DRD5_PSEU9 | A1DRD5)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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        A1DRD5_PSEU9 | A1DRD5: 3nqx 3nqy

(-) Related Entries Specified in the PDB File

3nqx VIBRIOLYSIN MCP-02
3nqy VIBRIOLYSIN MCP-02 WITH A SINGLE POINT MUTATION E346A