Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF SQUASH (CUCURBITA MOSCHATA) GLYCEROL-3-PHOSPHATE (1)-ACYLTRANSFERASE
 
Authors :  A. P. Turnbull, J. B. Rafferty, S. E. Sedelnikova, A. R. Slabas, T. P. Schierer, J. T. Kroon, J. W. Simon, T. Fawcett, I. Nishida, N. Murata, D. W. Rice
Date :  01 Oct 01  (Deposition) - 31 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Four-Helix Bundle, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. P. Turnbull, J. B. Rafferty, S. E. Sedelnikova, A. R. Slabas, T. P. Schierer, J. T. Kroon, J. W. Simon, T. Fawcett, I. Nishida, N. Murata, D. W. Rice
Analysis Of The Structure, Substrate Specificity, And Mechanism Of Squash Glycerol-3-Phosphate (1)-Acyltransferase.
Structure V. 9 347 2001
PubMed-ID: 11377195  |  Reference-DOI: 10.1016/S0969-2126(01)00595-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE
    ChainsA
    EC Number2.3.1.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET24A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePLSB
    Organism CommonCROOKNECK PUMPKIN
    Organism ScientificCUCURBITA MOSCHATA
    Organism Taxid3662
    SynonymGLYCEROL-3-PHOSPHATE (1)-ACYLTRANSFERASE, GPAT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1K30)

(-) Sites  (0, 0)

(no "Site" information available for 1K30)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K30)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K30)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K30)

(-) Exons   (0, 0)

(no "Exon" information available for 1K30)

(-) 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:363
 aligned with PLSB_CUCMO | P10349 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:366
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390      
           PLSB_CUCMO    31 AHSRKFLDVRSEEELLSCIKKETEAGKLPPNVAAGMEELYQNYRNAVIESGNPKADEIVLSNMTVALDRILLDVEDPFVFSSHHKAIREPFDYYIFGQNYIRPLIDFGNSFVGNLSLFKDIEEKLQQGHNVVLISNHQTEADPAIISLLLEKTNPYIAENTIFVAGDRVLADPLCKPFSIGRNLICVYSKKHMFDIPELTETKRKANTRSLKEMALLLRGGSQLIWIAPSGGRDRPDPSTGEWYPAPFDASSVDNMRRLIQHSDVPGHLFPLALLCHDIMPPPSQVEIEIGEKRVIAFNGAGLSVAPEISFEEIAATHKNPEEVREAYSKALFDSVAMQYNVLKTAISGKQGLGASTADVSLSQPW 396
               SCOP domains d1k30a_ A: Glycerol-3-phosphate (1)-acyltransferase                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1k30A01 A:3-78  [code=1.10.1200.50, no name defined]                        1k30A02 A:79-368 Glycerol-3-phosphate (1)-acyltransferase                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh......ee.......hhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh..hhhhhhhheeeeehhhhhh..hhhhhhh.eeeee...........hhhhhhhhhhhhhhhhhhhhhh...eeee.....................hhhhhhhhhhhhhhh...eeeeeeeeehhhhh...hhhhhhh---........eeee....hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1k30 A   3 SHSRKFLDVRSEEELLSCIKKETEAGKLPPNVAAGMEELYQNYRNAVIESGNPKADEIVLSNMTVALDRILLDVEDPFVFSSHHKAIREPFDYYIFGQNYIRPLIDFGNSFVGNLSLFKDIEEKLQQGHNVVLISNHQTEADPAIISLLLEKTNPYIAENTIFVAGDRVLADPLCKPFSIGRNLICVYSKKHMFDIPELTETKRKANTRSLKEMALLLRGGSQLIWIAPSGGRDRPDPSTGEWYPAPFDASSVDNMRRLIQHSDVPGHLFPLALLCHDIMPPPSQVEIEI---RVIAFNGAGLSVAPEISFEEIAATHKNPEEVREAYSKALFDSVAMQYNVLKTAISGKQGLGASTADVSLSQPW 368
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292   |   302       312       322       332       342       352       362      
                                                                                                                                                                                                                                                                                                                           292 296                                                                        

   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1K30)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLSB_CUCMO | P10349)
molecular function
    GO:0004366    glycerol-3-phosphate O-acyltransferase activity    Catalysis of the reaction: acyl-CoA + sn-glycerol 3-phosphate = CoA + 1-acyl-sn-glycerol 3-phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0016024    CDP-diacylglycerol biosynthetic process    The chemical reactions and pathways resulting in the formation of CDP-diacylglycerol, CDP-1,2-diacylglycerol, a substance composed of diacylglycerol in glycosidic linkage with cytidine diphosphate.
    GO:0006650    glycerophospholipid metabolic process    The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1k30)
 
  Sites
(no "Sites" information available for 1k30)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1k30)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1k30
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PLSB_CUCMO | P10349
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.3.1.15
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PLSB_CUCMO | P10349
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PLSB_CUCMO | P103491iuq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1K30)