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(-) Description

Title :  CRYSTAL STRUCTURE OF ACUTOLYSIN-C, A HEMORRHAGIC TOXIN FROM THE SNAKE VENOM OF AGKISTRODON ACUTUS, AT 2.2 A RESOLUTION
 
Authors :  L. Niu, M. Teng, X. Zhu
Date :  30 Jun 99  (Deposition) - 05 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Metalloprotease, Hemorrhagic Toxin, Snake Venom Proteinase, Crystal Structure, Agkistrodon Acutus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhu, M. Teng, L. Niu
Structure Of Acutolysin-C, A Haemorrhagic Toxin From The Venom Of Agkistrodon Acutus, Providing Further Evidence For The Mechanism Of The Ph-Dependent Proteolytic Reaction Of Zinc Metalloproteinases.
Acta Crystallogr. , Sect. D V. 55 1834 1999
PubMed-ID: 10531480  |  Reference-DOI: 10.1107/S0907444999010306
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACUTOLYSIN-C
    Chains: A
    Organism Common: CHINESE MOCCASIN
    Organism Scientific: DEINAGKISTRODON ACUTUS
    Organism Taxid: 36307
    Secretion: VENOM
    Synonym: HEMORRHAGIN III

 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
1AC1SOFTWAREHIS A:142 , HIS A:146 , HIS A:152 , HOH A:300BINDING SITE FOR RESIDUE ZN A 999

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:117 -A:195
2A:157 -A:179
3A:159 -A:162

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADAM_MEPROPS50215 ADAM type metalloprotease domain profile.VM1A3_DEIAC5-197  1A:6-198
VM11_DEIAC197-392  1A:6-195
2ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.VM1A3_DEIAC138-147  1A:139-148
VM11_DEIAC330-339  1A:139-148

(-) Exons   (0, 0)

(no "Exon" information available for 1QUA)

(-) 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:197
 aligned with VM11_DEIAC | Q9W7S2 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:198
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382        
           VM11_DEIAC   193 TWPQTSVNLQLIVDHSMYAKYNSNSEKITKTLQERVNIMKEIFKPLNLDITLSGIEMWDKKDLITVKTAATDTLKLFAKWRQTDLLKRIDNDNAQLQTAVDFDGETVGLAFKSTMCDKRYSAGIIQDHSAIPLLMAVTMAHELGHNLGMDHDDTSKCNCNVCIMAPRLNTNPSKTFSDCSNNDYQKFLTDKKPKCIHK 390
               SCOP domains d1quaa_ A: Snake venom metalloprotease                                                                                                                                                                 SCOP domains
               CATH domains 1quaA00 A:2-198 Collagenase (Catalytic Domain)                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee............hhhhhhhhhhhhhhhhhhh....eeeeee.........eee...........eeeee.....hhhhhhhhhhhhhhh.........-.....................hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ----ADAM_MEPRO  PDB: A:6-195 UniProt: 197-392                                                                                                                                                          PROSITE (2)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qua A   2 PAPQTSIELFLIVDHSMYAKYNSNSSKITTTLKARVNIMNAIYSSLNLVITLSGIEMWSAADLITVQSSSRNTLKLFASWRETDLLKRTSNDNAQLLTATNFNGNTVGLAYLKTMCNSKYSVGLIQDHSAIPLLMAVTMAHELGHNLGMNHDGAG-CSCATCIMAPVLSSGPAKSFSDCSKHDYQSFLTIHKPQCLLN 198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    | |160       170       180       190        
                                                                                                                                                                                    156 |                                         
                                                                                                                                                                                      157                                         


Chain A from PDB  Type:PROTEIN  Length:197
 aligned with VM1A3_DEIAC | P60244 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
          VM1A3_DEIAC     1 PAPQTSIELFLIVDHSMYAKYNSNSSKITTTLKARVNIMNAIYSSLNLVITLSGIEMWSAADLITVQSSSRNTLKLFASWRETDLLKRTSNDNAQLLTATNFNGNTVGLAYLKTMCNSKYSVGLIQDHSAIPLLMAVTMAHELGHNLGMNHDGAGCSCATCIMAPVLSSGPAKSFSDCSKHDYQSFLTIHKPQCLLN 197
               SCOP domains d1quaa_ A: Snake venom metalloprotease                                                                                                                                                                SCOP domains
               CATH domains 1quaA00 A:2-198 Collagenase (Catalytic Domain)                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee............hhhhhhhhhhhhhhhhhhh....eeeeee.........eee...........eeeee.....hhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ADAM_MEPRO  PDB: A:6-198 UniProt: 5-197                                                                                                                                                           PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qua A   2 PAPQTSIELFLIVDHSMYAKYNSNSSKITTTLKARVNIMNAIYSSLNLVITLSGIEMWSAADLITVQSSSRNTLKLFASWRETDLLKRTSNDNAQLLTATNFNGNTVGLAYLKTMCNSKYSVGLIQDHSAIPLLMAVTMAHELGHNLGMNHDGAGCSCATCIMAPVLSSGPAKSFSDCSKHDYQSFLTIHKPQCLLN 198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
   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  (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 1QUA)

(-) Gene Ontology  (9, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VM11_DEIAC | Q9W7S2)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.

Chain A   (VM1A3_DEIAC | P60244)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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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