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(-) Description

Title :  AN ALTERNATE DESCRIPTION OF A CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 FROM BUNGARUS CAERULEUS
 
Authors :  R. E. Stenkamp, I. Le Trong
Date :  06 Feb 07  (Deposition) - 06 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Phospholipase, Krait Venom, Structure Reinterpretation, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Le Trong, R. E. Stenkamp
An Alternate Description Of Two Crystal Structures Of Phospholipase A(2) From Bungarus Caeruleus.
Acta Crystallogr. , Sect. D V. 63 548 2007
PubMed-ID: 17372360  |  Reference-DOI: 10.1107/S0907444907007354
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2 ISOFORM 3
    Chains: A
    EC Number: 3.1.1.4
    Organism Scientific: BUNGARUS CAERULEUS
    Organism Taxid: 132961
    Secretion: VENOM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:82 , ALA A:83 , GLN A:120 , HOH A:149BINDING SITE FOR RESIDUE CL A 1
2AC2SOFTWAREGLY A:60 , MET A:112 , HOH A:134BINDING SITE FOR RESIDUE CL A 2
3AC3SOFTWARELYS A:31BINDING SITE FOR RESIDUE CL A 121

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:13 -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 2OSN)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B3_BUNCE61-68  1A:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B3_BUNCE107-117  1A:90-100

(-) Exons   (0, 0)

(no "Exon" information available for 2OSN)

(-) 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:118
 aligned with PA2B3_BUNCE | Q6SLM0 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:118
                                    29        39        49        59        69        79        89        99       109       119       129        
          PA2B3_BUNCE    20 NLQQFKNMIQCAGTRTWTAYINYGCYCGKGGSGTPVDKLDRCCYTHDHCYNQADSIPGCNPNIKTYSYTCTQPNITCTRTADACAKFLCDCDRTAAICFASAPYNINNIMISASNSCQ 137
               SCOP domains d2osna_ A: automated matches                                                                                           SCOP domains
               CATH domains 2osnA00 A:3-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhh................hhhhhhhhhhhhhhhhhhhh...........eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2osn A   3 NLQQFKNMIQCAGTRTWTAYINYGCYCGKGGSGTPVDKLDRCCYTHDHCYNQADSIPGCNPNIKTYSYTCTQPNITCTRTADACAKFLCDCDRTAAICFASAPYNINNIMISASNSCQ 120
                                    12        22        32        42        52        62        72        82        92       102       112
   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: 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 2OSN)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PA2B3_BUNCE | Q6SLM0)
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

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

UniProtKB/Swiss-Prot
        PA2B3_BUNCE | Q6SLM0: 1g2x

(-) Related Entries Specified in the PDB File

1fe5 A THIRD ISOFORM, ORIGINALLY REPORTED IN SPACE GROUP R32, AND ISOMORPHOUS TO THE CRYSTALS OF THE OTHER ISOFORMS.
1g2x THE SAME PROTEIN AND DATA SET, BUT INTERPRETED WITH A DIFFERENT SPACE GROUP SYMMETRY. RELATED ID: R1G2XSF RELATED DB: PDB THIS ENTRY 2OSN REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R1G2XSF
1u4j ANOTHER ISOFORM OF THE ENZYME, BUT ALSO LIKELY IN SPACE GROUP R32 RATHER THAN THE REPORTED R3.