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(-) Description

Title :  PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM
 
Authors :  B. W. Segelke, D. Nguyen, R. Chee, H. N. Xuong, E. A. Dennis
Date :  21 Jan 98  (Deposition) - 29 Apr 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Phospholipase, Trimer, Calcium Binding, Activator Site, Carboxylic Ester Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. W. Segelke, D. Nguyen, R. Chee, N. H. Xuong, E. A. Dennis
Structures Of Two Novel Crystal Forms Of Naja Naja Naja Phospholipase A2 Lacking Ca2+ Reveal Trimeric Packing.
J. Mol. Biol. V. 279 223 1998
PubMed-ID: 9636712  |  Reference-DOI: 10.1006/JMBI.1998.1759
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Cellular Location: VENOM SACK
    Chains: A, B, C
    EC Number: 3.1.1.4
    Organism Common: INDIAN COBRA
    Organism Scientific: NAJA NAJA
    Organism Taxid: 35670

 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 1A3F)

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1CAAUNKNOWNTYR A:27 , CYS A:28 , GLY A:29 , ARG A:30 , GLY A:31 , ASP A:48CA BINDING SITE.
2CABUNKNOWNTYR B:27 , CYS B:28 , GLY B:29 , ARG B:30 , GLY B:31 , ASP B:48CA BINDING SITE.
3CACUNKNOWNTYR C:27 , CYS C:28 , GLY C:29 , ARG C:30 , GLY C:31 , ASP C:48CA BINDING SITE.

(-) SS Bonds  (21, 21)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:71
2A:26 -A:118
3A:28 -A:44
4A:43 -A:99
5A:50 -A:92
6A:60 -A:85
7A:78 -A:90
8B:11 -B:71
9B:26 -B:118
10B:28 -B:44
11B:43 -B:99
12B:50 -B:92
13B:60 -B:85
14B:78 -B:90
15C:11 -C:71
16C:26 -C:118
17C:28 -C:44
18C:43 -C:99
19C:50 -C:92
20C:60 -C:85
21C:78 -C:90

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A3F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A3F)

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2A2_NAJNA43-50
 
 		  3A:43-50
B:43-50
C:43-50
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A2_NAJNA89-99
 
 		  3A:89-99
B:89-99
C:89-99

(-) Exons   (0, 0)

(no "Exon" information available for 1A3F)

(-) 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:119
 aligned with PA2A2_NAJNA | P15445 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
          PA2A2_NAJNA     1 NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 119
               SCOP domains d1a3fa_ A: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 1a3fA00 A:1-119 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhh.................hhhhhhhhhhhhhhhhhh............eee....eee.....hhhhhhhhhhhhhhhhhhh....hhh....hhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1a3f A   1 NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 119
                                    10        20        30        40        50        60        70        80        90       100       110         


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with PA2A2_NAJNA | P15445 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
          PA2A2_NAJNA     1 NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 119
               SCOP domains d1a3fb_ B: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 1a3fB00 B:1-119 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhh.................hhhhhhhhhhhhhhhhhh............eee....eee.....hhhhhhhhhhhhhhhhhhh....hhh....hhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1a3f B   1 NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 119
                                    10        20        30        40        50        60        70        80        90       100       110         


Chain C from PDB  Type:PROTEIN  Length:119
 aligned with PA2A2_NAJNA | P15445 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
          PA2A2_NAJNA     1 NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 119
               SCOP domains d1a3fc_ C: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 1a3fC00 C:1-119 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhh.................hhhhhhhhhhhhhhhhhh............eeee..eeee.....hhhhhhhhhhhhhhhhhhh....hhh....hhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1a3f C   1 NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 119
                                    10        20        30        40        50        60        70        80        90       100       110
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 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 1A3F)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (PA2A2_NAJNA | P15445)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        PA2A2_NAJNA | P15445: 1a3d 1ows 1psh 2wq5

(-) Related Entries Specified in the PDB File

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