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(-) Description

Title :  CRYSTAL STRUCTURE OF AAV-SP-I, A GLYCOSYLATED SNAKE VENOM SERINE PROTEINASE FROM AGKISTRODON ACUTUS
 
Authors :  Z. Zhu, M. Teng, L. Niu
Date :  04 Mar 03  (Deposition) - 25 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Snake Venom, Serine Proteinase, Glycoprotein, Agkistrodon Acutus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhu, Z. Liang, T. Zhang, Z. Zhu, W. Xu, M. Teng, L. Niu
Crystal Structures And Amidolytic Activities Of Two Glycosylated Snake Venom Serine Proteinases
J. Biol. Chem. V. 280 10524 2005
PubMed-ID: 15632114  |  Reference-DOI: 10.1074/JBC.M412900200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VENOM SERINE PROTEINASE
    Chains: A
    EC Number: 3.4.21.-
    Organism Common: CHINESE MOCCASIN
    Organism Scientific: DEINAGKISTRODON ACUTUS
    Organism Taxid: 36307
    Secretion: VENOM GLAND
    Synonym: SNAKE VENOM SERINE PROTEINASE, AAV-SP-I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:35 , THR A:36 , THR A:38 , FUC A:302 , NAG A:303BINDING SITE FOR RESIDUE NAG A 301
2AC2SOFTWAREHIS A:57 , ASP A:59 , SER A:60 , NAG A:301 , NAG A:303BINDING SITE FOR RESIDUE FUC A 302
3AC3SOFTWARENAG A:301 , FUC A:302BINDING SITE FOR RESIDUE NAG A 303
4AC4SOFTWAREHIS A:57 , GLY A:193 , SER A:195 , HOH A:690BINDING SITE FOR RESIDUE SO4 A 901
5AC5SOFTWARETHR A:145 , PRO A:146 , VAL A:147 , LYS A:148BINDING SITE FOR RESIDUE SO4 A 501

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:91 -A:245E
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:218 -Pro A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_VSPP_DEIAC_001 *D70NVSPP_DEIAC  ---  ---AD63N
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.VSPP_DEIAC25-249  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.VSPP_DEIAC61-66  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.VSPP_DEIAC198-209  1A:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1OP0)

(-) 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:234
 aligned with VSPP_DEIAC | Q9I8X1 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:234
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254    
          VSPP_DEIAC     25 VIGGNECDINEHRFLVAFFNTTGFFCGGTLINPEWVVTAAHCDSTDFQMQLGVHSKKVLNEDEQTRNPKEKFICPNKNNNEVLDKDIMLIKLDKPISNSKHIAPLSLPSSPPSVGSVCRIMGWGSITPVKETFPDVPYCANINLLDHAVCQAGYPELLAEYRTLCAGIVQGGKDTCGGDSGGPLICNGQFQGIVSYGAHPCGQGPKPGIYTNVFDYTDWIQRNIAGNTDATCPP  258
               SCOP domains d1op0a_ A: Venom serine protease                                                                                                                                                                                                           SCOP domains
               CATH domains 1op0A01     1op0A02 A:28-120,A:233-245 Trypsin-like serine proteases                                    1op0A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                       1op0A02      ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhh....eeee............eee.eeeeee..............eeeee........................eeeeee...............eeeeeeeehhhhhhhhh........eeeee...............eeee..eeeeeeee...........eeeee...hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------N-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 25-249                                                                                                                                                                                       --------- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1op0 A   16 VIGGNECDINEHRFLVAFFNTTGFFCGGTLINPEWVVTAAHCDSTDFQMQLGVHSKKVLNEDEQTRNPKEKFICPNKNNNEVLDKDIMLIKLDKPISNSKHIAPLSLPSSPPSVGSVCRIMGWGSITPVKETFPDVPYCANINLLDHAVCQAGYPELLAEYRTLCAGIVQGGKDTCGGDSGGPLICNGQFQGIVSYGAHPCGQGPKPGIYTNVFDYTDWIQRNIAGNTDATCPP 245G
                                    25        35||      46        56   ||   67        77        87        96       106       116       127 ||    138       148       158       168    |  177      186A|      195      |209       219  |    228       238      245C||||
                                               36|                    60|                               95A                           125| ||                                      172A           186A|             202|           221A                     245A||||||
                                                38                     62                                                              127 ||                                                      186B              207                                     245B|||||
                                                                                                                                         129|                                                                                                                 245C||||
                                                                                                                                          131                                                                                                                  245D|||
                                                                                                                                                                                                                                                                245E||
                                                                                                                                                                                                                                                                 245F|
                                                                                                                                                                                                                                                                  245G
   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: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OP0)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VSPP_DEIAC | Q9I8X1)
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: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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VSPP_DEIAC | Q9I8X1: 1op2

(-) Related Entries Specified in the PDB File

1op2 THE CRYSTAL STRUCTURE OF AAV-SP-II