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(-) Description

Title :  STRUCTURE OF PENTAVALENT PHOSPHOROUS INTERMEDIATE OF AN ENZYME CATALYZED PHOSPHORYL TRANSFER REACTION OBSERVED ON COCRYSTALLIZATION WITH GLUCOSE 6-PHOSPHATE
 
Authors :  S. D. Lahiri, G. Zhang, D. Dunaway-Mariano, K. N. Allen
Date :  20 Feb 03  (Deposition) - 18 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Haloacid Dehalogenase Superfamily, Phosphotransferase, Pentavalent Phosphate Intermediate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Lahiri, G. Zhang, D. Dunaway-Mariano, K. N. Allen
The Pentacovalent Phosphorus Intermediate Of A Phosphoryl Transfer Reaction.
Science V. 299 2067 2003
PubMed-ID: 12637673  |  Reference-DOI: 10.1126/SCIENCE.1082710
(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 BL21
    Expression System Strain: BL-21
    Expression System Taxid: 511693
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 1358

 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
1G161Ligand/IonALPHA-D-GLUCOSE 1,6-BISPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , LEU A:9 , ASP 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 , LYS A:145 , MG A:800 , HOH A:802 , HOH A:824 , HOH A:829 , HOH A:842 , HOH A:862 , HOH A:922 , HOH A:923BINDING SITE FOR RESIDUE G16 A 501
2AC2SOFTWAREASP A:8 , ASP A:10 , ASP A:170 , G16 A:501 , HOH A:824 , HOH A:922BINDING SITE FOR RESIDUE MG A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O03)

(-) 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 1O03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O03)

(-) Exons   (0, 0)

(no "Exon" information available for 1O03)

(-) 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 d1o03a_ A: beta-Phosphoglucomutase                                                                                                                                                                                            SCOP domains
               CATH domains 1o03A01       1o03A02 A:15-92 Putative phosphatase; domain 2                                1o03A01 A:1-14,A:93-221  [code=3.40.50.1000, no name defined]                                                                     CATH domains
               Pfam domains -Hydrolase-1o03A01 A:2-182                                                                                                                                                            --------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhh..eeee.....hhhhhhhhh.hhhhh.ee............hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.hhhhhh...eee.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o03 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)
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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  (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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  1o03
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 Related Entries

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

UniProtKB/Swiss-Prot
        PGMB_LACLA | P71447: 1lvh 1o08 1z4n 1z4o 1zol 2wf5 2wf6 2wf7 2wf8 2wf9 2wfa 2whe 3fm9 3zi4 4c4r 4c4s 4c4t

(-) Related Entries Specified in the PDB File

1lvh STRUCTURE OF UNLIGANDED BETA-PHOSPHOGLUCOMUTASE
1o08 PENTAVALENT PHOSPHOROUS INTERMEDIATE OF PHOSPHORYL TRANSFER REACTION