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 CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE FROM PYROCOCCUS FURIOSUS IN COMPLEX WITH MANNOSE 6-PHOSPHATE AND ZINC
 
Authors :  J. M. Berrisford, D. W. Rice, P. J. Baker
Date :  13 Mar 06  (Deposition) - 11 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cupin, Phosphoglucose Isomerase, Mannose 6-Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Berrisford, A. M. Hounslow, J. Akerboom, W. R. Hagen, S. J. Brouns, J. Van Der Oost, I. A. Murray, G. Michael Blackburn, J. P. Waltho, D. W. Rice, P. J. Baker
Evidence Supporting A Cis-Enediol-Based Mechanism For Pyrococcus Furiosus Phosphoglucose Isomerase
J. Mol. Biol. V. 358 1353 2006
PubMed-ID: 16580686  |  Reference-DOI: 10.1016/J.JMB.2006.03.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSE-6-PHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PLUW557
    Expression System Strain: BL21
    Expression System Taxid: 511693
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1M6P2Ligand/IonALPHA-D-MANNOSE-6-PHOSPHATE
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:88 , HIS B:90 , GLU B:97 , HIS B:136 , M6P B:502 , HOH B:669BINDING SITE FOR RESIDUE ZN B 401
2AC2SOFTWAREHIS A:88 , HIS A:90 , GLU A:97 , HIS A:136 , HOH A:676BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWARETYR A:52 , ALA A:69 , THR A:71 , LYS A:86 , GLY A:87 , HIS A:88 , GLU A:97 , TYR A:99 , ALA A:150 , TYR A:152 , HIS A:158 , TYR A:160 , HOH A:511 , HOH A:530 , HOH A:615 , HOH A:654 , HOH A:676BINDING SITE FOR RESIDUE M6P A 501
4AC4SOFTWARETYR B:52 , THR B:71 , THR B:85 , GLY B:87 , HIS B:88 , GLU B:97 , TYR B:99 , TYR B:152 , HIS B:158 , TYR B:160 , ZN B:401 , HOH B:509 , HOH B:562 , HOH B:595 , HOH B:605 , HOH B:669BINDING SITE FOR RESIDUE M6P B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GC3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GC3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GC3)

(-) Exons   (0, 0)

(no "Exon" information available for 2GC3)

(-) 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:188
 aligned with G6PI_PYRFU | P83194 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:188
                             1                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179        
           G6PI_PYRFU     - -MYKEPFGVKVDFETGIIEGAKKSVRRLSDMEGYFVDERAWKELVEKEDPVVYEVYAVEQEEKEGDLNFATTVLYPGKVGKEFFFTKGHFHAKLDRAEVYVALKGKGGMLLQTPEGDAKWISMEPGTVVYVPPYWAHRTVNIGDEPFIFLAIYPADAGHDYGTIAEKGFSKIVIEENGEVKVVDNPRW 187
               SCOP domains d2gc3a_ A: Glucose-6-phosphate isomerase, GPI                                                                                                                                                SCOP domains
               CATH domains 2gc3A00 A:0-187 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......hhhhhhhh..eeeeee..eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gc3 A   0 MMYKEPFGVKVDFETGIIEGAKKSVRRLSDMEGYFVDERAWKELVEKEDPVVYEVYAVEQEEKEGDLNFATTVLYPGKVGKEFFFTKGHFHAKLDRAEVYVALKGKGGMLLQTPEGDAKWISMEPGTVVYVPPYWAHRTVNIGDEPFIFLAIYPADAGHDYGTIAEKGFSKIVIEENGEVKVVDNPRW 187
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179        


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with G6PI_PYRFU | P83194 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:188
                             1                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179        
           G6PI_PYRFU     - -MYKEPFGVKVDFETGIIEGAKKSVRRLSDMEGYFVDERAWKELVEKEDPVVYEVYAVEQEEKEGDLNFATTVLYPGKVGKEFFFTKGHFHAKLDRAEVYVALKGKGGMLLQTPEGDAKWISMEPGTVVYVPPYWAHRTVNIGDEPFIFLAIYPADAGHDYGTIAEKGFSKIVIEENGEVKVVDNPRW 187
               SCOP domains d2gc3b_ B: Glucose-6-phosphate isomerase, GPI                                                                                                                                                SCOP domains
               CATH domains 2gc3B00 B:0-187 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..eeeeee..eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gc3 B   0 MMYKEPFGVKVDFETGIIEGAKKSVRRLSDMEGYFVDERAWKELVEKEDPVVYEVYAVEQEEKEGDLNFATTVLYPGKVGKEFFFTKGHFHAKLDRAEVYVALKGKGGMLLQTPEGDAKWISMEPGTVVYVPPYWAHRTVNIGDEPFIFLAIYPADAGHDYGTIAEKGFSKIVIEENGEVKVVDNPRW 187
                                     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)
    → 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 2GC3)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

 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
    M6P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gc3)
 

(-) 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
  2gc3
    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
  G6PI_PYRFU | P83194
    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)
  5.3.1.9
    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
  G6PI_PYRFU | P83194
    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
        G6PI_PYRFU | P83194: 1qxj 1qxr 1qy4 1x7n 1x82 1x8e 2gc0 2gc1 2gc2 3sxw 4lta 4luk 4lul 4lum

(-) Related Entries Specified in the PDB File

1x7n THE CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS PHOSPHOGLUCOSE ISOMERASE WITH BOUND 5-PHOSPHO-D-ARABINONATE AND MANGANESE
1x82 CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE FROM PYROCOCCUS FURIOSUS WITH BOUND 5-PHOSPHO-D-ARABINONATE
1x8e CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS PHOSPHOGLUCOSE ISOMERASE FREE ENZYME
2gc0 THE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE FROM PYROCOCCUS FURIOSUS IN COMPLEX WITH 5-PHOSPHO-D- ARABINONOHYDROXAMATE AND ZINC
2gc1 THE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE FROM PYROCOCCUS FURIOSUS IN COMPLEX WITH SORBITOL 6-PHOSPHATE AND ZINC
2gc2 THE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE FROM PYROCOCCUS FURIOSUS IN COMPLEX WITH FRUCTOSE 6-PHOSPHATE AND ZINC