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 :  STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE INHIBITED WITH GLUCOSE-6-PHOSPAHTE AND TRIFLUOROMAGNESATE
 
Authors :  M. W. Bowler, N. J. Baxter, C. E. Webster, A. M. Hounslow, M. J. Cliff, N. H. Williams, F. Hollfelder, S. Gamblin, G. M. Blackburn, J. P. Waltho
Date :  03 Apr 09  (Deposition) - 15 Sep 09  (Release) - 23 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Isomerase, Phosphotransferase, Magnesium Fluoride, Transition State Analogue, Haloacid Dehalogenase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. J. Baxter, M. W. Bowler, T. Alizadeh, M. J. Cliff, A. M. Hounslow, B. Wu, D. B. Berkowitz, N. H. Williams, G. M. Blackburn, J. P. Waltho
Atomic Details Of Near-Transition State Conformers For Enzyme Phosphoryl Transfer Revealed By Mgf-3 Rather Than By Phosphoranes.
Proc. Natl. Acad. Sci. Usa V. 107 4555 2010
PubMed-ID: 20164409  |  Reference-DOI: 10.1073/PNAS.0910333106

(-) Compounds

Molecule 1 - BETA-PHOSPHOGLUCOMUTASE
    Chains: A
    EC Number: 5.4.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 1358
    Strain: 19435
    Synonym: BETA-PGM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1BG61Ligand/IonBETA-D-GLUCOSE-6-PHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3MGF1Ligand/IonTRIFLUOROMAGNESATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , HIS A:20 , GLY A:46 , VAL A:47 , ARG A:49 , SER A:52 , SER A:114 , ALA A:115 , SER A:116 , LYS A:117 , ASN A:118 , HOH A:2055 , HOH A:2091 , HOH A:2200 , HOH A:2201 , HOH A:2202 , MGF A:2832BINDING SITE FOR RESIDUE BG6 A1831
2AC2SOFTWAREHOH A:2058 , HOH A:2060 , HOH A:2120 , HOH A:2121 , HOH A:2142 , HOH A:2143BINDING SITE FOR RESIDUE MG A2801
3AC3SOFTWAREASP A:8 , LEU A:9 , ASP A:10 , SER A:114 , ALA A:115 , LYS A:145 , BG6 A:1831 , HOH A:2170 , HOH A:2172 , MG A:2833BINDING SITE FOR RESIDUE MGF A2832
4AC4SOFTWAREASP A:8 , ASP A:10 , ASP A:170 , HOH A:2170 , HOH A:2172 , MGF A:2832BINDING SITE FOR RESIDUE MG A2833

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WF5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:60 -Asp A:61
2Lys A:145 -Pro A:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WF5)

(-) Exons   (0, 0)

(no "Exon" information available for 2WF5)

(-) 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:218
 aligned with PGMB_LACLA | P71447 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
           PGMB_LACLA     1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLEKMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSYYTLEFLKEVWLQ 218
               SCOP domains d2wf5a_ A: beta-Phosphoglucomutase                                                                                                                                                                                         SCOP domains
               CATH domains 2wf5A01       2wf5A02 A:15-92 Putative phosphatase; domain 2                                2wf5A01 A:1-14,A:93-218  [code=3.40.50.1000, no name defined]                                                                  CATH domains
               Pfam domains -Hydrolase-2wf5A01 A:2-182                                                                                                                                                            ------------------------------------ Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeee.....hhhhhhhhh.hhhhh.ee............hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.hhhhhh...eee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wf5 A   1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSHYTLEFLKEVWLQ 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PGMB_LACLA | P71447)
molecular function
    GO:0008801    beta-phosphoglucomutase activity    Catalysis of the reaction: beta-D-glucose 1-phosphate = beta-D-glucose 6-phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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.
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
    BG6  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MGF  [ 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
    Ala A:60 - Asp A:61   [ RasMol ]  
    Lys A:145 - Pro A:146   [ 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
  2wf5
    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
  PGMB_LACLA | P71447
    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)
  5.4.2.6
    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
  PGMB_LACLA | P71447
    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
        PGMB_LACLA | P71447: 1lvh 1o03 1o08 1z4n 1z4o 1zol 2wf6 2wf7 2wf8 2wf9 2wfa 2whe 3fm9 3zi4 4c4r 4c4s 4c4t

(-) Related Entries Specified in the PDB File

1lvh THE STRUCTURE OF PHOSPHORYLATED BETA- PHOSPHOGLUCOMUTASEFROM LACTOCCOCUS LACTIS TO 2. 3 ANGSTROM RESOLUTION
1o03 STRUCTURE OF PENTAVALENT PHOSPHOROUS INTERMEDIATE OF ANENZYME CATALYZED PHOSPHORYL TRANSFER REACTION OBSERVED ONCOCRYSTALLIZATION WITH GLUCOSE 6-PHOSPHATE
1o08 STRUCTURE OF PENTAVALENT PHOSPHOROUS INTERMEDIATE OF ANENZYME CATALYZED PHOSPHORYL TRANSFER REACTION OBSERVED ONCOCRYSTALLIZATION WITH GLUCOSE 1-PHOSPHATE
1z4n STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE WITH INHIBITOR BOUNDALPHA-GALACTOSE 1-PHOSPHATE COCRYSTALLIZED WITH FLUORIDE
1z4o STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE WITH INHIBITOR BOUNDALPHA-GALACTOSE 1-PHOSPHATE
1zol NATIVE BETA-PGM
2wf6 STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE INHIBITED WITH GLUCOSE-6-PHOSPAHTE AND ALUMINIUM TETRAFLUORIDE
2wf7 STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE INHIBITED WITH GLUCOSE-6-PHOSPHONATE AND ALUMINIUM TETRAFLUORIDE
2wf8 STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE INHIBITED WITH GLUCOSE-6-PHOSPHATE, GLUCOSE-1- PHOSPHATE AND BERYLLIUM TRIFLUORIDE
2wf9 STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE INHIBITED WITH GLUCOSE-6-PHOSPHATE, AND BERYLLIUM TRIFLUORIDE, CRYSTAL FORM 2
2wfa STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE INHIBITED WITH BERYLLIUM TRIFLUORIDE, IN AN OPEN CONFORMATION.
2whe STRUCTURE OF NATIVE BETA-PHOSPHOGLUCOMUTASE IN AN OPEN CONFORMATION WITHOUT BOUND LIGANDS.