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 :  CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS PHOSPHOGLUCOSE ISOMERASE
 
Authors :  J. -J. Jeong, S. Fushinobu, S. Ito, M. Hidaka, H. Shoun, T. Wakagi
Date :  11 Feb 03  (Deposition) - 24 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoglucose Isomerase, Cupin Superfamily, Iron Ion, Archaea (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. -J. Jeong, S. Fushinobu, S. Ito, M. Hidaka, H. Shoun, T. Wakagi
Crystal Structure Of A Novel Cupin-Type Phosphoglucose Isomerase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOGLUCOSE ISOMERASE
    ChainsA, B
    EC Number5.3.1.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET21D
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificTHERMOCOCCUS LITORALIS
    Organism Taxid2265

 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
1FE1Ligand/IonFE (III) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:89 , HIS A:91 , GLU A:98 , HIS A:159BINDING SITE FOR RESIDUE FE A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J3P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J3P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J3P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J3P)

(-) Exons   (0, 0)

(no "Exon" information available for 1J3P)

(-) 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:187
 aligned with G6PI_THELI | P84140 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
           G6PI_THELI     1 MKYKEPFGVKLDFETGIIENAKKSVRRLSDMKGYFIDEEAWKKMVEEGDPVVYEVYAIEQEEKEGDLNFATTVLYPGKVGNEFFMTKGHYHSKIDRAEVYFALKGKGGMLLQTPEGEARFIEMEPGTIVYVPPYWAHRTINTGDKPFIFLALYPADAGHDYGTIAEKGFSKIVVEENGKVVVKDNPK 187
               SCOP domains d1j3pa_ A: Glucose-6-phosphate isomerase, GPI                                                                                                                                               SCOP domains
               CATH domains 1j3pA00 A:1-187 Jelly Rolls                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...........eeeeee.hhhh....hhhhhhhhhhhh..eeeeeeee........eeeeeeee...ee..ee..............eeeeeee..eeeeee.....eeeeee...eeeee....eeeeee.....eeeeeeee......hhhhhhhh..eeeee...eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3p A   1 MKYKEPFGVKLDFETGIIENAKKSVRRLSDMKGYFIDEEAWKKMVEEGDPVVYEVYAIEQEEKEGDLNFATTVLYPGKVGNEFFMTKGHYHSKIDRAEVYFALKGKGGMLLQTPEGEARFIEMEPGTIVYVPPYWAHRTINTGDKPFIFLALYPADAGHDYGTIAEKGFSKIVVEENGKVVVKDNPK 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with G6PI_THELI | P84140 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:183
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   
           G6PI_THELI     3 YKEPFGVKLDFETGIIENAKKSVRRLSDMKGYFIDEEAWKKMVEEGDPVVYEVYAIEQEEKEGDLNFATTVLYPGKVGNEFFMTKGHYHSKIDRAEVYFALKGKGGMLLQTPEGEARFIEMEPGTIVYVPPYWAHRTINTGDKPFIFLALYPADAGHDYGTIAEKGFSKIVVEENGKVVVKDN 185
               SCOP domains d1j3pb_ B: Glucose-6-phosphate isomerase, GPI                                                                                                                                           SCOP domains
               CATH domains 1j3pB00 B:3-185 Jelly Rolls                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...........eeeeee.hhhh....hhhhhhhhhhh...eeeeeeee........eeeeeeee...ee..ee..............eeeeeee..eeeeee.....eeeeee...eeeee....eeeeee.....eeeeeeee......hhhhhhh...eeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3p B   3 YKEPFGVKLDFETGIIENAKKSVRRLSDMKGYFIDEEAWKKMVEEGDPVVYEVYAIEQEEKEGDLNFATTVLYPGKVGNEFFMTKGHYHSKIDRAEVYFALKGKGGMLLQTPEGEARFIEMEPGTIVYVPPYWAHRTINTGDKPFIFLALYPADAGHDYGTIAEKGFSKIVVEENGKVVVKDN 185
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J3P)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (G6PI_THELI | P84140)
molecular function
    GO:0004347    glucose-6-phosphate isomerase activity    Catalysis of the reaction: D-glucose 6-phosphate = D-fructose 6-phosphate.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1j3p)
 

(-) 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
  1j3p
    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
  G6PI_THELI | P84140
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.3.1.9
    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
  G6PI_THELI | P84140
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        G6PI_THELI | P841401j3q 1j3r

(-) Related Entries Specified in the PDB File

1j3q 1J3Q CONTAINS THE SAME PROTEIN COMPLEXED WITH 2 FE ION
1j3r 1J3R CONTAINS THE SAME PROTEIN COMPLEXED WITH FE AND 6PG