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(-) Description

Title :  SEQUENCE INDUCED TRIMERIZATION OF KRAIT PLA2: CRYSTAL STRUCTURE OF THE TRIMERIC FORM OF KRAIT PLA2
 
Authors :  G. Singh, S. Gourinath, S. Sharma, S. Bhanumathi, M. Paramsivam, T. P. Singh
Date :  22 Oct 00  (Deposition) - 17 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structure, Phospholipase A2, Homotrimer, Bungarus Caeruleus, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Singh, S. Gourinath, K. Saravanan, S. Sharma, S. Bhanumathi, C. H. Betzel, A. Srinivasan, T. P. Singh
Sequence-Induced Trimerization Of Phospholipase A2: Structure Of A Trimeric Isoform Of Pla2 From Common Krait (Bungarus Caeruleus) At 2. 5 A Resolution.
Acta Crystallogr. , Sect. F V. 61 8 2005
PubMed-ID: 16508078  |  Reference-DOI: 10.1107/S1744309104025503
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A, B, C
    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

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1G2X)

(-) Sites  (0, 0)

(no "Site" information available for 1G2X)

(-) SS Bonds  (21, 21)

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
15C:11 -C:72
16C:27 -C:119
17C:29 -C:45
18C:44 -C:100
19C:51 -C:93
20C:61 -C:86
21C:79 -C:91

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gln A:74 -Pro A:75
2Gln B:74 -Pro B:75
3Gln C:74 -Pro C:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G2X)

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B3_BUNCE61-68
 
 		  3A:44-51
B:44-51
C:44-51
PA2B_BUNCE69-76
 
 		  3A:44-51
B:44-51
C:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B3_BUNCE107-117
 
 		  3A:90-100
B:90-100
C:90-100
PA2B_BUNCE115-125
 
 		  3A:90-100
B:90-100
C:90-100

(-) Exons   (0, 0)

(no "Exon" information available for 1G2X)

(-) 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 d1g2xa_ A: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1g2xA00 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
                 1g2x A   1 NLQQFKNMIQCAGTRTWTAYINYGCYCGKGGSGTPVDKLDRCCYTHDHCYNQADSIPGCNPNIKTYSYTCTQPNITCTRTADACAKFLCDCDRTAAICFASAPYNINNIMISASNSCQ 120
                                    10  |||   22        32        42        52        62        72        82        92       102       112        
                                       13||                                                                                                       
                                        15|                                                                                                       
                                         17                                                                                                       


Chain A from PDB  Type:PROTEIN  Length:118
 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 d1g2xa_ A: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1g2xA00 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 (1) -----------------------------------------PA2_HIS --------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------PA2_ASP    -------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2x A   1 NLQQFKNMIQCAGTRTWTAYINYGCYCGKGGSGTPVDKLDRCCYTHDHCYNQADSIPGCNPNIKTYSYTCTQPNITCTRTADACAKFLCDCDRTAAICFASAPYNINNIMISASNSCQ 120
                                    10  |||   22        32        42        52        62        72        82        92       102       112        
                                       13||                                                                                                       
                                        15|                                                                                                       
                                         17                                                                                                       


Chain B 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 d1g2xb_ B: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1g2xB00 B:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2x B   1 NLQQFKNMIQCAGTRTWTAYINYGCYCGKGGSGTPVDKLDRCCYTHDHCYNQADSIPGCNPNIKTYSYTCTQPNITCTRTADACAKFLCDCDRTAAICFASAPYNINNIMISASNSCQ 120
                                    10  |||   22        32        42        52        62        72        82        92       102       112        
                                       13||                                                                                                       
                                        15|                                                                                                       
                                         17                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:118
 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 d1g2xb_ B: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1g2xB00 B:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------PA2_HIS --------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------PA2_ASP    -------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2x B   1 NLQQFKNMIQCAGTRTWTAYINYGCYCGKGGSGTPVDKLDRCCYTHDHCYNQADSIPGCNPNIKTYSYTCTQPNITCTRTADACAKFLCDCDRTAAICFASAPYNINNIMISASNSCQ 120
                                    10  |||   22        32        42        52        62        72        82        92       102       112        
                                       13||                                                                                                       
                                        15|                                                                                                       
                                         17                                                                                                       


Chain C 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 d1g2xc_ C: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1g2xC00 C:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2x C   1 NLQQFKNMIQCAGTRTWTAYINYGCYCGKGGSGTPVDKLDRCCYTHDHCYNQADSIPGCNPNIKTYSYTCTQPNITCTRTADACAKFLCDCDRTAAICFASAPYNINNIMISASNSCQ 120
                                    10  |||   22        32        42        52        62        72        82        92       102       112        
                                       13||                                                                                                       
                                        15|                                                                                                       
                                         17                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:118
 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 d1g2xc_ C: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1g2xC00 C:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------PA2_HIS --------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------PA2_ASP    -------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2x C   1 NLQQFKNMIQCAGTRTWTAYINYGCYCGKGGSGTPVDKLDRCCYTHDHCYNQADSIPGCNPNIKTYSYTCTQPNITCTRTADACAKFLCDCDRTAAICFASAPYNINNIMISASNSCQ 120
                                    10  |||   22        32        42        52        62        72        82        92       102       112        
                                       13||                                                                                                       
                                        15|                                                                                                       
                                         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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G2X)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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.

Chain A,B,C   (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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    Gln A:74 - Pro A:75   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        PA2B3_BUNCE | Q6SLM0: 2osn
        PA2B_BUNCE | Q9DF52: 1dpy 1fe5 1po8

(-) Related Entries Specified in the PDB File

1fe5 THREE DIMENSIONAL STRUCTURE OF A NOVEL PHOSPHOLIPASE A2 FROM INDIAN COMMON KRAIT AT 2.45 RESOLUTION
1g0z SPECIFIC MUTATIONS IN KRAIT PLA2 LEAD TO DIMERATION OF PROTEIN MOLECULES: CRYSTAL STRUCTURE OF KRAIT PLA2 AT 2.1 RESOLUTION