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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS PHOSPHOGLUCOSE ISOMERASE WITH BOUND 5-PHOSPHO-D-ARABINONATE AND MANGANESE
 
Authors :  J. M. Berrisford, J. Akerboom, S. Brouns, S. E. Sedelnikova, A. P. Turnb Der Oost, L. Salmon, R. Hardre, I. A. Murray, G. M. Blackburn, D. W. Ric P. J. Baker
Date :  16 Aug 04  (Deposition) - 12 Oct 04  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cupin Superfamily, Pyrococcus Furiosus, Hyperthermophile, Phosphoglucose Isomerase, Extremeophile, 5-Phospho-D-Arabinonate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Berrisford, J. Akerboom, S. Brouns, S. E. Sedelnikova, A. P. Turnbull, J. Van Der Oost, L. Salmon, R. Hardre, I. A. Murray, G. M. Blackburn, D. W. Rice, P. J. Baker
The Structures Of Inhibitor Complexes Of Pyrococcus Furiosu Phosphoglucose Isomerase Provide Insights Into Substrate Binding And Catalysis.
J. Mol. Biol. V. 343 649 2004
PubMed-ID: 15465052  |  Reference-DOI: 10.1016/J.JMB.2004.08.061

(-) Compounds

Molecule 1 - GLUCOSE-6-PHOSPHATE ISOMERASE
    Chains: A
    EC Number: 5.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PGIA
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: GPI, PHOSPHOGLUCOSE ISOMERASE, PGI, PHOSPHOHEXOSE ISOMERASE, PHI

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2PA51Ligand/Ion5-PHOSPHOARABINONIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2PA52Ligand/Ion5-PHOSPHOARABINONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:88 , HIS A:90 , GLU A:97 , HIS A:136 , PA5 A:301 , HOH A:407BINDING SITE FOR RESIDUE MN A 400
2AC2SOFTWARETYR A:52 , ALA A:69 , THR A:71 , THR A:85 , GLY A:87 , HIS A:88 , GLU A:97 , TYR A:99 , HIS A:136 , PHE A:148 , TYR A:152 , TYR A:160 , MN A:400 , HOH A:401 , HOH A:402 , HOH A:403 , HOH A:404 , HOH A:406 , HOH A:407BINDING SITE FOR RESIDUE PA5 A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X7N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X7N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X7N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X7N)

(-) Exons   (0, 0)

(no "Exon" information available for 1X7N)

(-) Sequences/Alignments

Asymmetric 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:189
 aligned with G6PI_PYRFU | P83194 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:189
                             1                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179         
           G6PI_PYRFU     - -MYKEPFGVKVDFETGIIEGAKKSVRRLSDMEGYFVDERAWKELVEKEDPVVYEVYAVEQEEKEGDLNFATTVLYPGKVGKEFFFTKGHFHAKLDRAEVYVALKGKGGMLLQTPEGDAKWISMEPGTVVYVPPYWAHRTVNIGDEPFIFLAIYPADAGHDYGTIAEKGFSKIVIEENGEVKVVDNPRWK 188
               SCOP domains d1x7na_ A: Glucose-6-phosphate isomerase, GPI                                                                                                                                                 SCOP domains
               CATH domains 1x7nA00 A:0-188 Jelly Rolls                                                                                                                                                                   CATH domains
               Pfam domains ------------------------GPI-1x7nA01 A:24-188                                                                                                                                                  Pfam domains
         Sec.struct. author .......................eeee.hhh.....hhhhhhhhhhhh..eeeeeeee........eeeeeeee...ee..ee..............eeeeeee..eeeeee.....eeeeee....eeee....eeeeee.....eeeeeeee......hhhhhhhh..eeeeee..eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x7n A   0 MMYKEPFGVKVDFETGIIEGAKKSVRRLSDMEGYFVDERAWKELVEKEDPVVYEVYAVEQEEKEGDLNFATTVLYPGKVGKEFFFTKGHFHAKLDRAEVYVALKGKGGMLLQTPEGDAKWISMEPGTVVYVPPYWAHRTVNIGDEPFIFLAIYPADAGHDYGTIAEKGFSKIVIEENGEVKVVDNPRWK 188
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (G6PI_PYRFU | P83194)
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1x7n
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  G6PI_PYRFU | P83194
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 Related Entries

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

UniProtKB/Swiss-Prot
        G6PI_PYRFU | P83194: 1qxj 1qxr 1qy4 1x82 1x8e 2gc0 2gc1 2gc2 2gc3 3sxw 4lta 4luk 4lul 4lum

(-) Related Entries Specified in the PDB File

1plz CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE FROM PYROCOCCUS FURIOSUS