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(-) Description

Title :  STRUCTURE-BASED DESIGN OF POTENT AND SELECTIVE INHIBITORS OF PHOSPHOLIPASE A2: CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PHOSHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AND A DESIGNED PEPTIDE INHIBITOR AT 1.9 A RESOLUTION
 
Authors :  R. K. Singh, P. Vikram, M. Paramsivam, T. Jabeen, S. Sharma, J. Makker, S P. Kaur, A. Srinivasan, T. P. Singh
Date :  09 Aug 02  (Deposition) - 30 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Naja Naja Sagittifera, Phospholipase A2, Designed Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Singh, P. Vikram, J. Makker, T. Jabeen, S. Sharma, S. Dey, P. Kaur, A. Srinivasan, T. P. Singh
Design Of Specific Peptide Inhibitors For Group I Phospholipase A2: Structure Of A Complex Formed Between Phospholipase A2 From Naja Naja Sagittifera (Group I) And A Designed Peptide Inhibitor Val-Ala-Phe-Arg-Ser (Vafrs) At 1. 9 A Resolution Reveals Unique Features
Biochemistry V. 42 11701 2003
PubMed-ID: 14529280  |  Reference-DOI: 10.1021/BI035076X
(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 - VAL-ALA-PHE-ARG-SER
    Chains: B
    Engineered: YES
    Other Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:28 , LYS A:31 , GLY A:32 , ASP A:49 , HOH A:244 , ARG B:4BINDING SITE FOR RESIDUE CA A 201
2AC2SOFTWAREPHE A:5 , LYS A:6 , ILE A:9 , TRP A:19 , PHE A:22 , ALA A:23 , TYR A:28 , GLY A:30 , LYS A:31 , ASP A:40 , ARG A:43 , CYS A:44 , CYS A:45 , THR A:47 , HIS A:48 , ASP A:49 , TYR A:64 , CYS A:100 , CA A:201 , HOH B:88BINDING SITE FOR CHAIN B OF VAL-ALA-PHE-ARG-SER

(-) SS Bonds  (7, 7)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MF4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MF4)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2A3_NAJSG50-57  1A:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A3_NAJSG96-106  1A:90-100

(-) Exons   (0, 0)

(no "Exon" information available for 1MF4)

(-) 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 PA2A3_NAJSG | P60045 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    17        27        37        47        57        67        77        87        97       107       117         
          PA2A3_NAJSG     8 NLYQFKNMIQCTVPSRSWQDFADYGCYCGKGGSGTPVDDLDRCCQVHDNCYNEAENISGCRPYFKTYSYECTQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDANYNIDLKARCN 126
               SCOP domains d1mf4a_ A: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 1mf4A00 A:1-120 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1mf4 A   1 NLYQFKNMIQCTVPSRSWADFADYGCYCGKGGSGTPVDDLDRCCQTHDNCYNEAENISGCRPYFKTYSYECTQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDANYNIDLKARCN 120
                                    10    ||  21        31        41        51        61        71        81        91       101       111         
                                         15|                                                                                                       
                                          17                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1mf4 B   1 VAFRS   5
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1MF4)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PA2A3_NAJSG | P60045)
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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  3.1.1.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        PA2A3_NAJSG | P60045: 1ln8 1oxr 1sz8 1t37 1td7 1yxl 1zm6 3gci 3jq5 3jql 3jti 3nju 3osh 3q4y

(-) 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 A RESOLUTION
1ln8 1LN8 IS THE CRYSTAL STRUCTURE OF A NEW ISOFORM OF PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AT 1.6 A RESOLUTION