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

(-) Description

Title :  THE 1.55 A CRYSTAL STRUCTURE OF GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE
 
Authors :  T. Tamada, M. D. Feese, Y. Kato, R. Kuroki
Date :  06 Mar 02  (Deposition) - 07 Oct 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Open Twisted Alpha/Beta, Four Helix Bundle, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tamada, M. D. Feese, S. R. Ferri, Y. Kato, R. Yajima, T. Toguri, R. Kuroki
Substrate Recognition And Selectivity Of Plant Glycerol-3-Phosphate Acyltransferases (Gpats) From Cucurbit Moscata And Spinacea Oleracea.
Acta Crystallogr. , Sect. D V. 60 13 2004
PubMed-ID: 14684887  |  Reference-DOI: 10.1107/S0907444903020778

(-) Compounds

Molecule 1 - GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE
    Chains: A
    EC Number: 2.3.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-17B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: CROOKNECK PUMPKIN
    Organism Scientific: CUCURBITA MOSCHATA
    Organism Taxid: 3662

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MSE7Mod. Amino AcidSELENOMETHIONINE
3SO45Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:80 , SER A:83 , HIS A:86 , HOH A:2164BINDING SITE FOR RESIDUE SO4 A 2001
02AC2SOFTWARELYS A:193 , HIS A:194 , GLY A:234 , ARG A:235 , ARG A:237 , GOL A:1005 , SO4 A:2004 , HOH A:2013 , HOH A:2119BINDING SITE FOR RESIDUE SO4 A 2002
03AC3SOFTWARESER A:3 , HIS A:4 , ARG A:6 , LYS A:154 , HOH A:2290BINDING SITE FOR RESIDUE SO4 A 2003
04AC4SOFTWARELYS A:193 , GLY A:234 , ARG A:235 , ALA A:248 , SO4 A:2002 , HOH A:2086BINDING SITE FOR RESIDUE SO4 A 2004
05AC5SOFTWARESER A:312 , PHE A:313 , GLU A:314 , HOH A:2309BINDING SITE FOR RESIDUE SO4 A 2005
06AC6SOFTWARESER A:63 , ASN A:64 , ASN A:101 , GLN A:353 , LEU A:355 , GLY A:356 , HOH A:2080 , HOH A:2089 , HOH A:2126BINDING SITE FOR RESIDUE GOL A 1001
07AC7SOFTWARELEU A:74 , ASP A:75 , ASP A:78 , PHE A:80 , ILE A:182 , HOH A:2047 , HOH A:2235 , HOH A:2306BINDING SITE FOR RESIDUE GOL A 1002
08AC8SOFTWARELYS A:87 , GLN A:225 , HOH A:2022 , HOH A:2046 , HOH A:2091 , HOH A:2123BINDING SITE FOR RESIDUE GOL A 1003
09AC9SOFTWAREPRO A:249 , PHE A:250 , ALA A:252 , GLU A:328 , SER A:331 , PHE A:335 , HOH A:2169BINDING SITE FOR RESIDUE GOL A 1004
10BC1SOFTWAREGLU A:142 , ASP A:169 , ARG A:170 , HIS A:194 , SO4 A:2002 , HOH A:2018 , HOH A:2243BINDING SITE FOR RESIDUE GOL A 1005
11BC2SOFTWARETYR A:246 , ALA A:339 , HOH A:2021 , HOH A:2095 , HOH A:2168 , HOH A:2211BINDING SITE FOR RESIDUE GOL A 1006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:91 -Pro A:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IUQ)

(-) 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:357
 aligned with PLSB_CUCMO | P10349 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:367
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       
           PLSB_CUCMO    30 PAHSRKFLDVRSEEELLSCIKKETEAGKLPPNVAAGMEELYQNYRNAVIESGNPKADEIVLSNMTVALDRILLDVEDPFVFSSHHKAIREPFDYYIFGQNYIRPLIDFGNSFVGNLSLFKDIEEKLQQGHNVVLISNHQTEADPAIISLLLEKTNPYIAENTIFVAGDRVLADPLCKPFSIGRNLICVYSKKHMFDIPELTETKRKANTRSLKEMALLLRGGSQLIWIAPSGGRDRPDPSTGEWYPAPFDASSVDNMRRLIQHSDVPGHLFPLALLCHDIMPPPSQVEIEIGEKRVIAFNGAGLSVAPEISFEEIAATHKNPEEVREAYSKALFDSVAMQYNVLKTAISGKQGLGASTADVSLSQPW 396
               SCOP domains d1iuqa_ A: Glycerol-3-phosphate (1)-acyltransferase                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1iuqA01 A:3-78  [code=1.10.1200.50, no name defined]                        1iuqA02 A:79-360 Glycerol-3-phosphate (1)-acyltransferase                                                                                                                                                                                                                                 -------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh......ee.......hhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh..hhhhhhhheeee.hhhhhh..hhhhhhh.eeee..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....................hhhhhhhhhhhhhh....eeeeeeeeehhhhh...----------........eeee....hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iuq A   2 ASHSRKFLDVRSEEELLSCIKKETEAGKLPPNVAAGmEELYQNYRNAVIESGNPKADEIVLSNmTVALDRILLDVEDPFVFSSHHKAIREPFDYYIFGQNYIRPLIDFGNSFVGNLSLFKDIEEKLQQGHNVVLISNHQTEADPAIISLLLEKTNPYIAENTIFVAGDRVLADPLCKPFSIGRNLICVYSKKHmFDIPELTETKRKANTRSLKEmALLLRGGSQLIWIAPSGGRDRPDPSTGEWYPAPFDASSVDNmRRLIQHSDVPGHLFPLALLCHDImPPP----------RVIAFNGAGLSVAPEISFEEIAATHKNPEEVREAYSKALFDSVAmQYNVLKTAISGKQGLGASTADVSLSQPW 368
                                    11        21        31      | 41        51        61   |    71        81        91       101       111       121       131       141       151       161       171       181       191   |   201       211    |  221       231       241       251      |261       271       281|  |     -    |  301       311       321       331       341       351       361       
                                                               38-MSE                     65-MSE                                                                                                                           195-MSE              216-MSE                                   258-MSE                 282-MSE       296                                         340-MSE                        
                                                                                                                                                                                                                                                                                                                     285
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:91 - Pro A:92   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1iuq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PLSB_CUCMO | P10349
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.3.1.15
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PLSB_CUCMO | P10349
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PLSB_CUCMO | P10349: 1k30

(-) Related Entries Specified in the PDB File

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