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(-) Description

Title :  SPECIFIC MUTATIONS IN KRAIT PLA2 LEAD TO DIMERIZATION OF PROTEIN MOLECULES: CRYSTAL STRUCTURE OF KRAIT PLA2 AT 2.1 RESOLUTION
 
Authors :  T. P. Singh, S. Gourinath, S. Sharma, G. Singh
Date :  10 Oct 00  (Deposition) - 17 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structure, Phospholipase A2, Homodimer, Bungarus Caeruleus, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Gourinath, G. Singh, S. Sharma, S. Bhanumathi, C. Betzel, M. Paramsivam, A. Srinivasan, T. P. Singh
Specific Mutations In Krait Pla2 Lead To Dimerization Of Protein Molecules: Crystal Structure Of Krait Pla2 At 2. 1 Resolution.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A, B
    EC Number: 3.1.1.4
    Fragment: RESIDUES 28-145
    Organism Scientific: BUNGARUS CAERULEUS
    Organism Taxid: 132961
    Other Details: NATURAL PROTEIN-ISOFORM
    Secretion: VENOM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:82 , SER B:83 , HOH B:186BINDING SITE FOR RESIDUE CL B 121
2AC2SOFTWARETHR A:82 , SER A:83 , HOH A:167BINDING SITE FOR RESIDUE CL A 121

(-) SS Bonds  (14, 14)

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
8B:11 -B:72
9B:27 -B:119
10B:29 -B:45
11B:44 -B:100
12B:51 -B:93
13B:61 -B:86
14B:79 -B:91

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:74 -Pro A:75
2Lys B:74 -Pro B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G0Z)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B5_BUNCE61-68
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B5_BUNCE107-117
 		  2A:90-100
B:90-100

(-) Exons   (0, 0)

(no "Exon" information available for 1G0Z)

(-) 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 PA2B5_BUNCE | Q6SLM1 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:118
                                    29        39        49        59        69        79        89        99       109       119       129        
          PA2B5_BUNCE    20 NLKQFKNMIQCAGTRTWTSYIGYGCYCGYGGSGTPVDELDRCCYTHDHCYNKAANIPGCNPLIKTYSYTCTKPNITCNDTSDSCARFICDCDRTAAICFASAPYNINNIMISASTSCQ 137
               SCOP domains d1g0za_ A: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1g0zA00 A:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1g0z A   1 NLKQFKNMIQCAGTRTWTSYIGYGCYCGYGGSGTPVDELDRCCYTHDHCYNKAANIPGCNPLIKTYSYTCTKPNITCNDTSDSCARFICDCDRTAAICFASAPYNINNIMISASTSCQ 120
                                    10   ||   22        32        42        52        62        72        82        92       102       112        
                                        14|                                                                                                       
                                         17                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PA2B5_BUNCE | Q6SLM1 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:118
                                    29        39        49        59        69        79        89        99       109       119       129        
          PA2B5_BUNCE    20 NLKQFKNMIQCAGTRTWTSYIGYGCYCGYGGSGTPVDELDRCCYTHDHCYNKAANIPGCNPLIKTYSYTCTKPNITCNDTSDSCARFICDCDRTAAICFASAPYNINNIMISASTSCQ 137
               SCOP domains d1g0zb_ B: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1g0zB00 B:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhh................hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1g0z B   1 NLKQFKNMIQCAGTRTWTSYIGYGCYCGYGGSGTPVDELDRCCYTHDHCYNKAANIPGCNPLIKTYSYTCTKPNITCNDTSDSCARFICDCDRTAAICFASAPYNINNIMISASTSCQ 120
                                    10   ||   22        32        42        52        62        72        82        92       102       112        
                                        14|                                                                                                       
                                         17
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G0Z)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PA2B5_BUNCE | Q6SLM1)
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.
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

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        PA2B5_BUNCE | Q6SLM1: 1u4j

(-) Related Entries Specified in the PDB File

1fe5 THREE DIMENSIONAL STRUCTURE OF A NOVEL PHOSPHOLIPASE A2 FROM INDIAN COMMON KRAIT AT 2.45 RESOLUTION