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(-) Description

Title :  STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE IN COMPLEX WITH AN ALPHA-FLUOROPHOSPHONATE ANALOGUE OF BETA-GLUCOSE-1-PHOSPHATE AND MAGNESIUM TRIFLUORIDE
 
Authors :  E. Pellegrini, M. W. Bowler
Date :  09 Sep 13  (Deposition) - 16 Jul 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Isomerase, Phosphoryl Transfer, Transition State, Metal Fluoride, Mutase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Jin, D. Bhattasali, E. Pellegrini, S. M. Forget, N. J. Baxter, M. J. Cliff, M. W. Bowler, D. L. Jakeman, G. M. Blackburn, J. P. Waltho
Alpha-Fluorophosphonates Reveal How A Phosphomutase Conserves Transition State Conformation Over Hexose Recognition In Its Two-Step Reaction.
Proc. Natl. Acad. Sci. Usa V. 111 12384 2014
PubMed-ID: 25104750  |  Reference-DOI: 10.1073/PNAS.1402850111

(-) Compounds

Molecule 1 - BETA-PHOSPHOGLUCOMUTASE
    Atcc: 19435
    Chains: A
    EC Number: 5.4.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET20A
    Expression System Vector Type: PLASMID
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 1358
    Synonym: BETA-PGM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GRX1Ligand/Ion(S)-1-BETA-PHOSPHONOFLUOROMETHYLENE-1-DEOXY-D-GLUCOPYRANOSE
2MG1Ligand/IonMAGNESIUM ION
3MGF1Ligand/IonTRIFLUOROMAGNESATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , ASP A:10 , ASP A:170 , MGF A:1220 , HOH A:2009 , HOH A:2011BINDING SITE FOR RESIDUE MG A2833
2AC2SOFTWAREASP A:10 , HIS A:20 , TRP A:24 , LEU A:44 , LYS A:45 , GLY A:46 , VAL A:47 , SER A:48 , ARG A:49 , SER A:52 , LYS A:76 , SER A:116 , LYS A:117 , ASN A:118 , MGF A:1220 , HOH A:2109 , HOH A:2151 , HOH A:2296BINDING SITE FOR RESIDUE GRX A1219
3AC3SOFTWAREASP A:8 , LEU A:9 , ASP A:10 , SER A:114 , ALA A:115 , LYS A:145 , GRX A:1219 , HOH A:2009 , HOH A:2011 , MG A:2833BINDING SITE FOR RESIDUE MGF A1220

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C4S)

(-) 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 4C4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C4S)

(-) Exons   (0, 0)

(no "Exon" information available for 4C4S)

(-) 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:215
 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhh.---..hhhhhhhhhhhhhhhhhhhh...hhhh...hhhhhhhhhhhh..eeee.....hhhhhhhhh.hhhhh.ee............hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.hhhhhh...eee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c4s A   1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDL---KVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSHYTLEFLKEVWLQ 218
                                    10        20        30        40        50        |-  |     70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
                                                                                     59  63
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4C4S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C4S)

(-) 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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    Lys A:145 - Pro A:146   [ RasMol ]  
 

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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 3fm9 3zi4 4c4r 4c4t

(-) Related Entries Specified in the PDB File

4c4r STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE IN COMPLEX WITH A PHOSPHONATE ANALOGUE OF BETA-GLUCOSE-1-PHOSPHATE AND MAGNESIUM TRIFLUORIDE
4c4t STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE IN COMPLEX WITH A PHOSPHONATE ANALOGUE OF BETA-GLUCOSE-1-PHOSPHATE AND ALUMINIUM TETRAFLUORIDE