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(-) Description

Title :  CRYSTAL STRUCTURE OF LYS49-PHOSPHOLIPASE A2 FROM AGKISTRODON CONTORTRIX LATICINCTUS, FATTY ACID BOUND FORM
 
Authors :  A. L. B. Ambrosio, D. H. F. De Souza, M. C. Nonato, H. S. Selistre De Ara C. L. Ownby, R. C. Garratt
Date :  02 Feb 04  (Deposition) - 10 Feb 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Lys49-Phospholipase A2, Snake Venom, Myotoxicity, Fatty Acid Bound Form, Hydrolase, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. B. Ambrosio, M. C. Nonato, H. S. Selistre De Araujo, R. Arni, R. J. Ward, C. L. Ownby, D. H. F. De Souza, R. C. Garratt
A Molecular Mechanism For Lys49-Phospholipase A2 Activity Based On Ligand-Induced Conformational Change.
J. Biol. Chem. V. 280 7326 2005
PubMed-ID: 15596433  |  Reference-DOI: 10.1074/JBC.M410588200

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2 HOMOLOG
    Chains: A
    EC Number: 3.1.1.4
    Organism Common: BROAD-BANDED COPPERHEAD
    Organism Scientific: AGKISTRODON CONTORTRIX LATICINCTUS
    Organism Taxid: 37195
    Other Details: SNAKE VENOM PROTEIN
    Strain: LATICINCTUS
    Synonym: MYOTOXIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1DAO1Ligand/IonLAURIC ACID
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:33 , ARG A:34 , LYS A:53BINDING SITE FOR RESIDUE SO4 A 134
2AC2SOFTWARELEU A:2 , LEU A:3 , GLY A:6 , ILE A:9 , ALA A:18 , TYR A:22 , GLY A:30 , CYS A:45 , VAL A:102 , PHE A:124 , GOL A:136BINDING SITE FOR RESIDUE DAO A 135
3AC3SOFTWARELEU A:5 , GLY A:30 , HIS A:48 , TYR A:52 , DAO A:135 , HOH A:266BINDING SITE FOR RESIDUE GOL A 136

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:27 -A:126
2A:29 -A:45
3A:44 -A:105
4A:50 -A:133
5A:51 -A:98
6A:61 -A:91
7A:84 -A:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S8G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S8G)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2H1_AGKCL59-66  1A:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2H1_AGKCL101-111  1A:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 1S8G)

(-) 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:121
 aligned with PA2H1_AGKCL | P49121 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:121
                                    26        36        46        56        66        76        86        96       106       116       126       136 
          PA2H1_AGKCL    17 SLLELGKMILQETGKNAITSYGSYGCNCGWGHRGQPKDATDRCCFVHKCCYKKLTDCNHKTDRYSYSWKNKAIICEEKNPCLKEMCECDKAVAICLRENLDTYNKKYKAYFKFKCKKPETC 137
               SCOP domains d1s8ga_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1s8gA00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eee....eee...hhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s8g A   1 SLLELGKMILQETGKNAITSYGSYGCNCGWGHRGQPKDATDRCCFVHKCCYKKLTDCNHKTDRYSYSWKNKAIICEEKNPCLKEMCECDKAVAICLRENLDTYNKKYKAYFKFKCKKPETC 133
                                    10   ||   21        31        41        51    ||||69        79    ||  90       100       110       120 || || 132 
                                        14|                                      56|||               84|                                 122| ||     
                                         16                                       59||                86                                  124 ||     
                                                                                   61|                                                      126|     
                                                                                    67                                                       128
   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 alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1S8G)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PA2H1_AGKCL | P49121)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004623    phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
biological process
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
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
        PA2H1_AGKCL | P49121: 1s8h 1s8i

(-) Related Entries Specified in the PDB File

1s8h 1s8i