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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS PHOSPHOGRUCOSE ISOMERASE COMPLEXED WITH GLUCONATE-6-PHOSPHATE
 
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 :  2.18
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoglucose Isomerase, Cupin Superfamily, Iron Ion, Archaea, Gluconate 6-Phosphate (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
    Chains: A, B
    EC Number: 5.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21D
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOCOCCUS LITORALIS
    Organism Taxid: 2265

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
16PG2Ligand/Ion6-PHOSPHOGLUCONIC ACID
2FE1Ligand/IonFE (III) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:53 , VAL A:55 , ALA A:70 , THR A:72 , THR A:86 , LYS A:87 , GLY A:88 , HIS A:89 , GLU A:98 , TYR A:100 , PHE A:149 , TYR A:153 , HIS A:159 , TYR A:161 , FE A:201 , HOH A:603 , HOH A:606 , HOH A:620 , HOH A:655 , HOH A:684 , HOH A:691BINDING SITE FOR RESIDUE 6PG A 600
2AC2SOFTWARETYR B:53 , THR B:72 , THR B:86 , LYS B:87 , GLY B:88 , HIS B:89 , GLU B:98 , TYR B:100 , TYR B:153 , HIS B:159 , TYR B:161 , HOH B:602 , HOH B:617 , HOH B:631 , HOH B:633 , HOH B:676BINDING SITE FOR RESIDUE 6PG B 601
3AC3SOFTWAREHIS A:89 , HIS A:91 , GLU A:98 , 6PG A:600 , HOH A:624BINDING SITE FOR RESIDUE FE A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J3R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J3R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J3R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J3R)

(-) Exons   (0, 0)

(no "Exon" information available for 1J3R)

(-) 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 d1j3ra_ A: Glucose-6-phosphate isomerase, GPI                                                                                                                                               SCOP domains
               CATH domains 1j3rA00 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
                 1j3r 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:185
 aligned with G6PI_THELI | P84140 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:185
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182     
           G6PI_THELI     3 YKEPFGVKLDFETGIIENAKKSVRRLSDMKGYFIDEEAWKKMVEEGDPVVYEVYAIEQEEKEGDLNFATTVLYPGKVGNEFFMTKGHYHSKIDRAEVYFALKGKGGMLLQTPEGEARFIEMEPGTIVYVPPYWAHRTINTGDKPFIFLALYPADAGHDYGTIAEKGFSKIVVEENGKVVVKDNPK 187
               SCOP domains d1j3rb_ B: Glucose-6-phosphate isomerase, GPI                                                                                                                                             SCOP domains
               CATH domains 1j3rB00 B:3-187 Jelly Rolls                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...........eeeeee.hhh.....hhhhhhhhhhhh..eeeeeeee........eeeeeeee...ee..ee..............eeeeeee..eeeeee.....eeeeee...eeeee....eeeeee.....eeeeeeee......hhhhhhh...eeeee...eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3r B   3 YKEPFGVKLDFETGIIENAKKSVRRLSDMKGYFIDEEAWKKMVEEGDPVVYEVYAIEQEEKEGDLNFATTVLYPGKVGNEFFMTKGHYHSKIDRAEVYFALKGKGGMLLQTPEGEARFIEMEPGTIVYVPPYWAHRTINTGDKPFIFLALYPADAGHDYGTIAEKGFSKIVVEENGKVVVKDNPK 187
                                    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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J3R)

(-) 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        G6PI_THELI | P84140: 1j3p 1j3q

(-) Related Entries Specified in the PDB File

1j3p 1J3P CONTAINS THE SAME PROTEIN COMPLEXED WITH 1 FE ION
1j3q 1J3Q CONTAINS THE SAME PROTEIN COMPLEXED WITH 2 FE ION