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(-) Description

Title :  CRYSTAL STRUCTURE OF A ZINC CONTAINING DIMER OF PHOSPHOLIPASE A2 FROM THE VENOM OF INDIAN COBRA (NAJA NAJA SAGITTIFERA)
 
Authors :  T. Jabeen, A. K. Varma, M. Paramasivam, N. Singh, R. K. Singh, S. Sharma, A. Srinivasan, T. P. Singh
Date :  19 Aug 02  (Deposition) - 20 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phospholipase A2, Enzyme, Phospholipids, Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Jabeen, A. K. Varma, M. Paramasivam, N. Singh, R. K. Singh, S. Sharma, A. Srinivasan, T. P. Singh
Crystal Structure Of A Zinc Containing Dimer Of Phospholipase A2 From The Venom Of Indian Cobra (Naja Naja Saggittifera)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A
    EC Number: 3.1.1.4
    Organism Scientific: NAJA SAGITTIFERA
    Organism Taxid: 195058
    Secretion: VENOM
 
Molecule 2 - PHOSPHOLIPASE A2
    Chains: B
    EC Number: 3.1.1.4
    Organism Scientific: NAJA SAGITTIFERA
    Organism Taxid: 195058
    Secretion: VENOM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:24 , ASN A:112 , HOH A:303 , ASP B:24 , ASN B:112 , HOH B:160BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREHIS A:48 , ASP A:49 , LYS A:64 , ARG B:31BINDING SITE FOR RESIDUE ACY A 302

(-) 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  (0, 0)

(no "Cis Peptide Bond" information available for 1MH2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MH2)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2A2_NAJSG50-57  1B:44-51
PA2B1_NAJSG50-57  1A:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A2_NAJSG96-106  1B:90-100
PA2B1_NAJSG96-106  1A:91-100

(-) Exons   (0, 0)

(no "Exon" information available for 1MH2)

(-) 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 PA2B1_NAJSG | P60043 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    17        27        37        47        57        67        77        87        97       107       117         
          PA2B1_NAJSG     8 NTYQFKNMIQCTVPKRSWWDFADYGCYCGRGGSGTPIDDLDRCCQVHDNCYNSAREQGGCRPKQKTYSYECKAGTLSCSGSNNSCAATVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 126
               SCOP domains d1mh2a_ A: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 1mh2A00 A:1-120 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh...............hhhhhhhhhhhhhhhhh..............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1mh2 A   1 NTYQFQNMIQCTVPKRSWRDFADYGCYCGRGGSGTPIDDLDSCCQVHDNCYNSAREQGGCRPKQKTYTYQCKAGGLSCSGANNSCAATTCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 120
                                    10    ||  21        31        41        51        61        71        81        91       101       111         
                                         15|                                                                                                       
                                          17                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with PA2A2_NAJSG | P60044 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    17        27        37        47        57        67        77        87        97       107       117         
          PA2A2_NAJSG     8 NRWQFKNMISCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCNPRFRTYSYECTAGTLTCTGRNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLQARCN 126
               SCOP domains d1mh2b_ B: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 1mh2B00 B: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 (2) ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1mh2 B   1 NTWQFKNMISCTVPSRSWWDFADYGCYCGRGGSGTPSDDLDRCCQTHDNCYNEAEKISGCNPRFRTYSYACTAGTLTCTGRNNACAASVCDCDRNAAICFAGAPYNDSNYNIDLQARCN 120
                                    10    ||  21        31        41        51        61        71        81        91       101       111         
                                         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  (2, 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 1MH2)

(-) Gene Ontology  (7, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PA2B1_NAJSG | P60043)
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.

Chain B   (PA2A2_NAJSG | P60044)
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_NAJSG | P60044: 1s6b 1xxw 2rd4
        PA2B1_NAJSG | P60043: 1mh7 1mh8 1s6b 1xxw 2rd4

(-) Related Entries Specified in the PDB File

1lff 1LFF IS THE CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AT 1.5 RESOLUTION
1lfj 1LFJ IS THE X-RAY CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN TWO HOMOLOGOUS ISOFORMS OF PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA : PRINCIPLE OF MOLECULAR ASSOCIATION AND INACTIVATION
1ln8 1LN8 IS THE CRYSTAL STRUCTURE OF A NEW ISOFORM OF PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AT 1.6 RESOLUTION
1mf4 1MF4 IS THE STRUCTURE BASED DESIGN OF POTENT AND SELECTIVE INHIBITORS OF PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AND A DESIGNED PEPTIDE INHIBITOR AT 1.9 A RESOLUTION