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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N1A MUTANT OF HUMAN GROUP IIA PHOSPHOLIPASE A2
 
Authors :  S. H. Edwards, D. Thompson, S. F. Baker, S. P. Wood, D. C. Wilton
Date :  22 Oct 02  (Deposition) - 28 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. H. Edwards, D. Thompson, S. F. Baker, S. P. Wood, D. C. Wilton
The Crystal Structure Of The H48Q Active Site Mutant Of Human Group Iia Secreted Phospholipase A2 At 1. 5 A Resolution Provides An Insight Into The Catalytic Mechanism
Biochemistry V. 41 15468 2002
PubMed-ID: 12501175  |  Reference-DOI: 10.1021/BI020485Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2, MEMBRANE ASSOCIATED
    ChainsA
    EC Number3.1.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11A
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, GROUP IIA PHOSPHOLIPASE A2, GIIC SPLA2, NON-PANCREATIC SECRETORY PHOSPHOLIPASE A2, NPS-PLA2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:27 , GLY A:29 , GLY A:31 , ASP A:48BINDING SITE FOR RESIDUE CA A 125
2AC2SOFTWAREPHE A:23 , GLY A:25 , TYR A:112 , ASN A:114BINDING SITE FOR RESIDUE CA A 126

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:117
2A:28 -A:44
3A:43 -A:97
4A:49 -A:124
5A:50 -A:90
6A:59 -A:83
7A:77 -A:88

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N29)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N29)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2GA_HUMAN63-70  1A:43-50
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2GA_HUMAN107-117  1A:87-97

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2cENST000004005202cENSE00001543334chr1:20306111-2030607339PA2GA_HUMAN-00--
1.3cENST000004005203cENSE00002182826chr1:20305372-20305227146PA2GA_HUMAN1-14140--
1.3eENST000004005203eENSE00001326822chr1:20305017-20304873145PA2GA_HUMAN14-62491A:1-4242
1.3gENST000004005203gENSE00000873019chr1:20304614-20304508107PA2GA_HUMAN62-98371A:42-7837
1.4dENST000004005204dENSE00001543318chr1:20302336-20301929408PA2GA_HUMAN98-144471A:78-12447

(-) 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:124
 aligned with PA2GA_HUMAN | P14555 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:124
                                    30        40        50        60        70        80        90       100       110       120       130       140    
          PA2GA_HUMAN    21 NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 144
               SCOP domains d1n29a_ A: Phospholipase A2                                                                                                  SCOP domains
               CATH domains 1n29A00 A:1-124 Phospholipase A2                                                                                             CATH domains
               Pfam domains -Phospholip_A2_1-1n29A01 A:2-120                                                                                        ---- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhh..........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ------------------------------------PA2_ASP    --------------------------- PROSITE
           Transcript 1 (1) Exon 1.3e  PDB: A:1-42 UniProt: 14-62     -----------------------------------Exon 1.4d  PDB: A:78-124 UniProt: 98-144        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3g  PDB: A:42-78              ---------------------------------------------- Transcript 1 (2)
                 1n29 A   1 ALVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PA2GA_HUMAN | P14555)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0047498    calcium-dependent phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate. This reaction requires 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.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
biological process
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    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.
    GO:0034374    low-density lipoprotein particle remodeling    The acquisition, loss or modification of a protein or lipid within a low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.
    GO:0006654    phosphatidic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
    GO:0046473    phosphatidic acid metabolic process    The chemical reactions and pathways involving phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
    GO:0036151    phosphatidylcholine acyl-chain remodeling    Remodeling the acyl chains of phosphatidylcholine, through sequential deacylation and re-acylation reactions, to generate phosphatidylcholine containing different types of fatty acid acyl chains.
    GO:0036152    phosphatidylethanolamine acyl-chain remodeling    Remodeling the acyl chains of phosphatidylethanolamine, through sequential deacylation and re-acylation reactions, to generate phosphatidylethanolamine containing different types of fatty acid acyl chains.
    GO:0036148    phosphatidylglycerol acyl-chain remodeling    Remodeling the acyl chains of phosphatidylglycerol, through sequential deacylation and re-acylation reactions, to generate phosphatidylglycerol containing different types of fatty acid acyl chains.
    GO:0036149    phosphatidylinositol acyl-chain remodeling    Remodeling the acyl chains of phosphatidylinositol, through sequential deacylation and re-acylation reactions, to generate phosphatidylinositol containing different types of fatty acid acyl chains.
    GO:0036150    phosphatidylserine acyl-chain remodeling    Remodeling the acyl chains of phosphatidylserine, through sequential deacylation and re-acylation reactions, to generate phosphatidylserine containing different types of fatty acid acyl chains.
    GO:0006644    phospholipid metabolic process    The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0010744    positive regulation of macrophage derived foam cell differentiation    Any process that increases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PA2GA_HUMAN | P145551ayp 1bbc 1db4 1db5 1dcy 1j1a 1kqu 1kvo 1n28 1pod 1poe 2gny 3u8b 3u8d 3u8h 3u8i 5g3n

(-) Related Entries Specified in the PDB File

1n28 CRYSTAL STRUCTURE OF THE H48Q MUTANT OF HUMAN GROUP IIA PHOSPHOLIPASE A2