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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF A NOVEL PHOSPHOLIPASE A2 FROM INDIAN COMMON KRAIT AT 2.45 A RESOLUTION
 
Authors :  G. Singh, S. Gourinath, S. Sharma, M. Paramasivam, A. Srinivasan, T. P. Singh
Date :  28 Dec 99  (Deposition) - 28 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Indian Common Krait Venom, Phospholipase A2, Crystal Structure, Refinement, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Singh, S. Gourinath, S. Sharma, M. Paramasivam, A. Srinivasan, T. P. Singh
Sequence And Crystal Structure Determination Of A Basic Phospholipase A2 From Common Krait (Bungarus Caeruleus) At 2. 4 A Resolution: Identification And Characterization Of Its Pharmacological Sites.
J. Mol. Biol. V. 307 1049 2001
PubMed-ID: 11286555  |  Reference-DOI: 10.1006/JMBI.2001.4550
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    ChainsA
    EC Number3.1.1.4
    Organism ScientificBUNGARUS CAERULEUS
    Organism Taxid132961
    SecretionVENOM
    SynonymPLA2

 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
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:28 , GLY A:30 , GLY A:32 , ASP A:49 , HOH A:252BINDING SITE FOR RESIDUE NA A 150

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:72
2A:27 -A:119
3A:29 -A:45
4A:44 -A:100
5A:51 -A:93
6A:61 -A:86
7A:79 -A:91

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:74 -Pro A:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B_BUNCE69-76  1A:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B_BUNCE115-125  1A:90-100

(-) Exons   (0, 0)

(no "Exon" information available for 1DPY)

(-) 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:117
 aligned with PA2B_BUNCE | Q9DF52 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:118
                                    37        47        57        67        77        87        97       107       117       127       137        
           PA2B_BUNCE    28 NLIQFKNMIQCAGTRPWTAYVNYGCYCGKGGSGTPVDELDRCCYTHDNCYNEAEKIPGCNPNIKTYSYTCTEPNLTCTDTADTCARFLCDCDRTAAICFASAPYNSNNVMISSSTNCQ 145
               SCOP domains d1dpya_ A: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1dpyA00 A:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhh...-...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1dpy A   1 NLIQFKNMIQCAGTRIWTAYVAYGCYCGKGGSGTPVDELDRCCYTHDHCYNEAEKIPGCNPNIKTYSYTCTQPNLTCTDSADTCAQFLCECDRTAAICFASAPYNSNNIML-SSTSCQ 120
                                    10   ||   22        32        42        52        62        72        82        92       102       112| |     
                                        14|                                                                                             113 |     
                                         17                                                                                               115     

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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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PA2B_BUNCE | Q9DF52)
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: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.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
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.
    GO:0072556    other organism presynaptic membrane    A presynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A presynaptic membrane is specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

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 Related Entries

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UniProtKB/Swiss-Prot
        PA2B_BUNCE | Q9DF521fe5 1g2x 1po8

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