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(-) Description

Title :  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
 
Authors :  T. Jabeen, S. Sharma, R. K. Singh, P. Kaur, T. P. Singh
Date :  23 Jan 04  (Deposition) - 10 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phospholipase A2, Molecular Conformation, Enzyme Activity, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Jabeen, S. Sharma, N. Singh, R. K. Singh, P. Kaur, M. Perbandt, C. H. Betzel, A. Srinivasan, T. P. Singh
Crystal Structure Of A Calcium-Induced Dimer Of Two Isoforms Of Cobra Phospholipase A2 At 1. 6 A Resolution.
Proteins V. 59 856 2005
PubMed-ID: 15828003  |  Reference-DOI: 10.1002/PROT.20464
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2CA2Ligand/IonCALCIUM ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:24 , ASN A:112 , HOH A:537 , ASP B:24 , ASN B:112 , HOH B:715BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWARETYR B:28 , GLY B:30 , GLY B:32 , ASP B:49 , PO4 B:501 , HOH B:627BINDING SITE FOR RESIDUE CA B 402
3AC3SOFTWARETYR B:28 , CYS B:29 , GLY B:30 , CYS B:45 , HIS B:48 , ASP B:49 , CA B:402 , HOH B:673 , HOH B:697 , HOH B:799BINDING SITE FOR RESIDUE PO4 B 501
4AC4SOFTWAREASN A:1 , TYR A:3 , GLN A:65 , HOH A:606 , ASN B:109 , HOH B:731BINDING SITE FOR RESIDUE PO4 A 502
5AC5SOFTWAREGLY B:32 , HOH B:674 , HOH B:745BINDING SITE FOR RESIDUE ACY B 601
6AC6SOFTWAREHOH B:634 , HOH B:702 , HOH B:718 , HOH B:775 , HOH B:784BINDING SITE FOR RESIDUE ACY B 602

(-) 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 1S6B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S6B)

(-) 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:90-100

(-) Exons   (0, 0)

(no "Exon" information available for 1S6B)

(-) 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 d1s6ba_ A: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 1s6bA00 A:1-120 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhh..............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1s6b A   1 NTYQFKNMIQCTVPKRSWWDFADYGCYCGRGGSGTPIDDLDRCCQVHDNCYNSAREQGGCRPKQKTYSYECKAGTLSCSGSNNSCAATVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 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 d1s6bb_ B: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 1s6bB00 B:1-120 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1s6b B   1 NRWQFKNMISCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCNPRFRTYSYECTAGTLTCTGRNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLQARCN 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 1S6B)

(-) 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: 1mh2 1xxw 2rd4
        PA2B1_NAJSG | P60043: 1mh2 1mh7 1mh8 1xxw 2rd4

(-) Related Entries Specified in the PDB File

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