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(-) Description

Title :  CRYSTAL STRUCTURE OF BEE-VENOM PHOSPHOLIPASE A2 IN A COMPLEX WITH A TRANSITION-STATE ANALOGUE
 
Authors :  D. L. Scott, Z. Otwinowski, P. B. Sigler
Date :  07 Sep 92  (Deposition) - 31 Oct 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Scott, Z. Otwinowski, M. H. Gelb, P. B. Sigler
Crystal Structure Of Bee-Venom Phospholipase A2 In A Complex With A Transition-State Analogue.
Science V. 250 1563 1990
PubMed-ID: 2274788
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A
    EC Number: 3.1.1.4
    Engineered: YES
    Organism Common: HONEY BEE
    Organism Scientific: APIS MELLIFERA
    Organism Taxid: 7460

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GEL1Ligand/Ion1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GEL2Ligand/Ion1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:8 , GLY A:10 , GLY A:12 , ASP A:35 , GEL A:420BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREILE A:1 , TRP A:8 , GLY A:10 , HIS A:11 , GLY A:12 , HIS A:34 , ASP A:35 , THR A:57 , PHE A:67 , PHE A:82 , MET A:86 , TYR A:87 , CA A:501BINDING SITE FOR RESIDUE GEL A 420
3CA1UNKNOWNTRP A:8 , GLY A:10 , GLY A:12 , ASP A:35NULL

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:9 -A:31
2A:30 -A:70
3A:37 -A:63
4A:61 -A:95
5A:105 -A:113

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2_APIME63-70  1A:30-37
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2_APIME63-70  2A:30-37

(-) Exons   (0, 0)

(no "Exon" information available for 1POC)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:134
 aligned with PA2_APIME | P00630 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:134
                                    43        53        63        73        83        93       103       113       123       133       143       153       163    
            PA2_APIME    34 IIYPGTLWCGHGNKSSGPNELGRFKHTDACCRTHDMCPDVMSAGESKHGLTNTASHTRLSCDCDDKFYDCLKNSADTISSYFVGKMYFNLIDTKCYKLEHPVTGCGERTEGRCLHYTVDKSKPKVYQWFDLRKY 167
               SCOP domains d1poca_ A: Phospholipase A2                                                                                                            SCOP domains
               CATH domains 1pocA00 A:1-134 Phospholipase A2                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhh..ee....ee..ee......ee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eeeee..eee............ee......eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------PA2_HIS ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1poc A   1 IIYPGTLWCGHGNKSSGPNELGRFKHTDACCRTHDMCPDVMSAGESKHGLTNTASHTRLSCDCDDKFYDCLKNSADTISSYFVGKMYFNLIDTKCYKLEHPVTGCGERTEGRCLHYTVDKSKPKVYQWFDLRKY 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
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  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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (PA2_APIME | P00630)
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.

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