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(-) Description

Title :  A RE-DETERMINATION OF THE STRUCTURE OF THE TRIPLE MUTANT (K53,56,120M) OF PHOSPHOLIPASE A2 AT 1.6A RESOLUTION USING SULPHUR-SAS AT 1.54A WAVELENGTH
 
Authors :  K. Sekar, D. Velmurugan, V. Rajakannan, T. Yamane, M. Dauter, Z. Dauter
Date :  12 Jun 04  (Deposition) - 31 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha Helix, Beta Sheet, Triple Mutant, Calcium Ion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Sekar, V. Rajakannan, D. Velmurugan, T. Yamane, R. Thirumurugan, M. Dauter, Z. Dauter
A Redetermination Of The Structure Of The Triple Mutant (K53, 56, 120M) Of Phospholipase A2 At 1. 6 A Resolution Using Sulfur-Sas At 1. 54 A Wavelength.
Acta Crystallogr. , Sect. D V. 60 1586 2004
PubMed-ID: 15333929  |  Reference-DOI: 10.1107/S090744490401697X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A
    EC Number: 3.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTO-A2MBL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, GROUP IB PHOSPHOLIPASE A2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:28 , GLY A:30 , GLY A:32 , ASP A:49 , HOH A:245 , HOH A:248BINDING SITE FOR RESIDUE CA A 224
2AC2SOFTWARELYS A:12 , ILE A:82 , ILE A:104 , HOH A:332BINDING SITE FOR RESIDUE CL A 225
3AC3SOFTWAREPHE A:5 , PHE A:22 , GLY A:30 , HOH A:245BINDING SITE FOR RESIDUE MPD A 226
4AC4SOFTWARELEU A:19 , LYS A:108BINDING SITE FOR RESIDUE MPD A 227
5AC5SOFTWARESER A:15 , ASP A:21 , GLN A:54 , PHE A:94 , HOH A:265BINDING SITE FOR RESIDUE MPD A 228

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:77
2A:27 -A:123
3A:29 -A:45
4A:44 -A:105
5A:51 -A:98
6A:61 -A:91
7A:84 -A:96

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA21B_BOVIN66-73  1A:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA21B_BOVIN117-127  1A:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 1VKQ)

(-) 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:123
 aligned with PA21B_BOVIN | P00593 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:123
                                    32        42        52        62        72        82        92       102       112       122       132       142   
          PA21B_BOVIN    23 ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYKQAKKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDKKNC 145
               SCOP domains d1vkqa_ A: Phospholipase A2                                                                                                 SCOP domains
               CATH domains 1vkqA00 A:1-123 Phospholipase A2                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh................hhhhhhhhhhhhhhhhhhhh................eeee..eeee....hhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    ------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vkq A   1 ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYMQAMKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDMKNC 123
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
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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, 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 1VKQ)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PA21B_BOVIN | P00593)
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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  1vkq
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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
        PA21B_BOVIN | P00593: 1bp2 1bpq 1bvm 1c74 1ceh 1fdk 1g4i 1gh4 1irb 1kvw 1kvx 1kvy 1mks 1mkt 1mku 1mkv 1o2e 1o3w 1une 1vl9 2b96 2bax 2bch 2bd1 2bp2 2bpp 2zp3 2zp4 2zp5 3bp2 4bp2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VKQ)