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(-) Description

Title :  STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE INHIBITED WITH BERYLLIUM TRIFLUORIDE, IN AN OPEN CONFORMATION.
 
Authors :  M. W. Bowler, N. J. Baxter, C. E. Webster, S. Pollard, T. Alizadeh, A. M. Hounslow, M. J. Cliff, W. Bermel, N. H. Williams, F. Hollfelder, G. M. Blackburn, J. P. Waltho
Date :  03 Apr 09  (Deposition) - 26 May 10  (Release) - 16 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Isomerase, Phosphotransferase, Transition State Analogue, Haloacid Dehalogenase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Griffin, M. W. Bowler, N. J. Baxter, K. N. Leigh, H. R. Dannatt, A. M. Hounslow, G. M. Blackburn, C. E. Webster, M. J. Cliff, J. P. Waltho
Near Attack Conformers Dominate Beta-Phosphoglucomutase Complexes Where Geometry And Charge Distribution Reflect Those Of Substrate.
Proc. Natl. Acad. Sci. Usa V. 109 6910 2012
PubMed-ID: 22505741  |  Reference-DOI: 10.1073/PNAS.1116855109

(-) 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  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BEF1Ligand/IonBERYLLIUM TRIFLUORIDE ION
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , ASP A:10 , ASP A:170 , BEF A:1223 , HOH A:2152 , HOH A:2154BINDING SITE FOR RESIDUE MG A1222
2AC2SOFTWAREASP A:8 , LEU A:9 , ASP A:10 , SER A:114 , ALA A:115 , LYS A:145 , MG A:1222 , HOH A:2106 , HOH A:2139 , HOH A:2152 , HOH A:2154BINDING SITE FOR RESIDUE BEF A1223

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:145 -Pro A:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WFA)

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

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
           PGMB_LACLA     1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLEKMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSYYTLEFLKEVWLQKQK 221
               SCOP domains d2wfaa_ A: beta-Phosphoglucomutase                                                                                                                                                                                            SCOP domains
               CATH domains 2wfaA01       2wfaA02 A:15-92 Putative phosphatase; domain 2                                2wfaA01 A:1-14,A:93-221  [code=3.40.50.1000, no name defined]                                                                     CATH domains
               Pfam domains -Hydrolase-2wfaA01 A:2-182                                                                                                                                                            --------------------------------------- Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeee.....hhhhhhhhh.hhhhh.ee.hhhhh......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.hhhhhh...eee.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfa A   1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSHYTLEFLKEVWLQKQK 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PGMB_LACLA | P71447: 1lvh 1o03 1o08 1z4n 1z4o 1zol 2wf5 2wf6 2wf7 2wf8 2wf9 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
2wf5 STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE INHIBITED WITH GLUCOSE-6-PHOSPAHTE AND TRIFLUOROMAGNESATE
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