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(-) Description

Title :  CRYSTAL STRUCTURE OF BMOOMPALPHA-I, A NON-HEMORRHAGIC METALLOPROTEINASE ISOLATED FROM BOTHROPS MOOJENI SNAKE VENOM
 
Authors :  P. K. Akao, C. C. C. Tonoli, M. T. Murakami
Date :  20 Feb 09  (Deposition) - 22 Sep 09  (Release) - 16 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A
Keywords :  Snake Venom Metalloproteinase, Hydrolase, Metal-Binding, Metalloprotease, Protease, Secreted, Toxin, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. K. Akao, C. C. Tonoli, M. S. Navarro, A. C. Cintra, J. R. Neto, R. K. Arni, M. T. Murakami
Structural Studies Of Bmoompalpha-I, A Non-Hemorrhagic Metalloproteinase From Bothrops Moojeni Venom.
Toxicon V. 55 361 2010
PubMed-ID: 19706302  |  Reference-DOI: 10.1016/J.TOXICON.2009.08.013

(-) Compounds

Molecule 1 - ZINC METALLOPROTEINASE BMOOMPALFA-I
    Chains: A
    EC Number: 3.4.24.-
    Organism Common: LANCE-HEADED VIPER
    Organism Scientific: BOTHROPS MOOJENI
    Organism Taxid: 98334
    Tissue: VENOM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

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
1AC1SOFTWAREGLU A:7 , ASP A:91 , CYS A:195 , ASN A:198 , HOH A:405 , HOH A:410BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREHIS A:140 , HIS A:144 , HIS A:150 , HOH A:531 , HOH A:543 , HOH A:544BINDING SITE FOR RESIDUE ZN A 302

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:115 -A:195
2A:155 -A:179
3A:157 -A:162

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GBO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADAM_MEPROPS50215 ADAM type metalloprotease domain profile.VM1BI_BOTMO8-204  1A:4-200
2ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.VM1BI_BOTMO141-150  1A:137-146

(-) Exons   (0, 0)

(no "Exon" information available for 3GBO)

(-) 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:200
 aligned with VM1BI_BOTMO | P85314 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:200
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204
          VM1BI_BOTMO     5 FSPRYIELVVVADHGMFKKYNSNLNTIRKWVHEMVNSMNGFYRSVDVTASLANLEVWSKKDLINVQKDSRETLKSFGEWRERDLLPRISHDNAQLLTAIVFDGHTIGRAYTGGMCDPRHSVGVVMDHSPKNLQVAVTMAHELGHNLGMHHDGNQCHCDAASCIMADSLSVVLSYEFSDCSQNQYQTYLTKHNPQCILNEP 204
               SCOP domains d3gboa_ A: automated matches                                                                                                                                                                             SCOP domains
               CATH domains 3gboA00 A:1-200 Collagenase (Catalytic Domain)                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.eee...........eeeee....hhhhhhhhhhhhhhhhh..............ee...........ee.hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ADAM_MEPRO  PDB: A:4-200 UniProt: 8-204                                                                                                                                                               PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gbo A   1 FSPRHIELVVVADHGMFKKYNSNLNTIRKWVHEMVNSMNGFYRSVDVTASLANLEVWSKKDLINVQKDSRETLKSFGEWRERDLLPRISHDNAQLLTTIVFDGHVIGRAFTGGMCDPRHSVGVVMDHSPKNLQVAVTMAHELGHNLGMHHDGNQCHCDAASCIMADSLSQVLSYEFSDCSQNQYQTYLTKHNPQCILNEP 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GBO)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VM1BI_BOTMO | P85314)
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.
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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