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(-) Description

Title :  ANALYSIS OF THE STRUCTURAL DETERMINANTS UNDERLYING DISCRIMINATION BETWEEN SUBSTRATE AND SOLVENT IN BETA-PHOSPHOGLUCOMUTASE CATALYSIS
 
Authors :  L. Finci, S. Lahiri, E. Peisach, K. N. Allen
Date :  19 Dec 08  (Deposition) - 09 Jun 09  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Had Superfamily, Phosphoaspartate, Induced Fit, Domain Movement, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Dai, L. Finci, C. Zhang, S. Lahiri, G. Zhang, E. Peisach, K. N. Allen, D. Dunaway-Mariano
Analysis Of The Structural Determinants Underlying Discrimination Between Substrate And Solvent In Beta-Phosphoglucomutase Catalysis.
Biochemistry V. 48 1984 2009
PubMed-ID: 19154134  |  Reference-DOI: 10.1021/BI801653R
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-PHOSPHOGLUCOMUTASE
    Chains: A
    EC Number: 5.4.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: L0001, LL0429, PGMB
    Mutation: YES
    Organism Common: STREPTOCOCCUS LACTIS
    Organism Scientific: LACTOCOCCUS LACTIS SUBSP. LACTIS
    Organism Taxid: 1360
    Synonym: BETA-PGM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , ASP A:10 , GLU A:169 , ASP A:170BINDING SITE FOR RESIDUE MG A 222

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FM9)

(-) 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 3FM9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FM9)

(-) Exons   (0, 0)

(no "Exon" information available for 3FM9)

(-) 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:220
 aligned with PGMB_LACLA | P71447 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:220
                                    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 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLEKMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSYYTLEFLKEVWLQKQ 220
               SCOP domains d3fm9a_ A: beta-Phosphoglucomutase                                                                                                                                                                                           SCOP domains
               CATH domains 3fm9A01       3fm9A02 A:15-92 Putative phosphatase; domain 2                                3fm9A01 A:1-14,A:93-220  [code=3.40.50.1000, no name defined]                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh.ee............hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.hhhhhh...eee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fm9 A   1 MFKAVLFDLDGVITDPAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSHYTLEFLKEVWLQKQ 220
                                    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)
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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/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  (0, 0)

(no "Pfam Domain" information available for 3FM9)

(-) 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 2wfa 2whe 3zi4 4c4r 4c4s 4c4t

(-) Related Entries Specified in the PDB File

1lvh 1oo8