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(-) Description

Title :  STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE WITH INHIBITOR BOUND ALPHA-GALACTOSE 1-PHOSPHATE COCRYSTALLIZED WITH FLUORIDE
 
Authors :  L. W. Tremblay, G. Zhang, J. Dai, D. Dunaway-Mariano, K. N. Allen
Date :  16 Mar 05  (Deposition) - 19 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Isomerase, Beta-Phosphoglucomutase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. W. Tremblay, G. Zhang, J. Dai, D. Dunaway-Mariano, K. N. Allen
Chemical Confirmation Of A Pentavalent Phosphorane In Complex With Beta-Phosphoglucomutase
J. Am. Chem. Soc. V. 127 5298 2005
PubMed-ID: 15826149  |  Reference-DOI: 10.1021/JA0509073
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-PHOSPHOGLUCOMUTASE
    Chains: A, B
    EC Number: 5.4.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ISOMERASE
    Gene: PGMB
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 1358
    Synonym: BETA-PGM

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GL12Ligand/Ion1-O-PHOSPHONO-ALPHA-D-GALACTOPYRANOSE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GL11Ligand/Ion1-O-PHOSPHONO-ALPHA-D-GALACTOPYRANOSE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GL11Ligand/Ion1-O-PHOSPHONO-ALPHA-D-GALACTOPYRANOSE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , ASP A:10 , GLU A:169 , ASP A:170 , HOH A:1311BINDING SITE FOR RESIDUE MG A 800
2AC2SOFTWAREASP B:8 , ASP B:10 , GLU B:169 , ASP B:170 , HOH B:1279BINDING SITE FOR RESIDUE MG B 801
3AC3SOFTWAREHIS A:20 , TRP A:24 , LEU A:44 , GLY A:46 , VAL A:47 , ARG A:49 , LYS A:76 , ALA A:115 , SER A:116 , LYS A:117 , ASN A:118 , HOH A:1224 , HOH A:1225 , HOH A:1229 , HOH A:1241 , HOH A:1249 , HOH A:1270 , HOH A:1354BINDING SITE FOR RESIDUE GL1 A 1220
4AC4SOFTWAREHIS B:20 , TRP B:24 , LEU B:44 , GLY B:46 , VAL B:47 , ARG B:49 , LYS B:76 , ALA B:115 , SER B:116 , LYS B:117 , ASN B:118 , HOH B:1223 , HOH B:1227 , HOH B:1230 , HOH B:1231 , HOH B:1237 , HOH B:1246 , HOH B:1327BINDING SITE FOR RESIDUE GL1 B 1221

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z4N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:145 -Pro A:146
2Lys B:145 -Pro B:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z4N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z4N)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z4N)

(-) Sequences/Alignments

Asymmetric 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:219
 aligned with PGMB_LACLA | P71447 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           PGMB_LACLA     1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLEKMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSYYTLEFLKEVWLQK 219
               SCOP domains d1z4na_ A: beta-Phosphoglucomutase                                                                                                                                                                                          SCOP domains
               CATH domains 1z4nA01       1z4nA02 A:15-92 Putative phosphatase; domain 2                                1z4nA01 A:1-14,A:93-219  [code=3.40.50.1000, no name defined]                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhhhhhhh.......hhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhh..eeee.....hhhhhhhhh.hhhhh.ee.hhhhh......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.hhhhhh...eee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z4n A   1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSHYTLEFLKEVWLQK 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with PGMB_LACLA | P71447 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
           PGMB_LACLA     1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLEKMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSYYTLEFLKEVW 216
               SCOP domains d1z4nb_ B: beta-Phosphoglucomutase                                                                                                                                                                                       SCOP domains
               CATH domains 1z4nB01       1z4nB02 B:15-92 Putative phosphatase; domain 2                                1z4n            B01 B:1-14,B:93-216  [code=3.40.50.1000, no name defined]                                                    CATH domains
           Pfam domains (1) -Hydrolase-1z4nB01 B:2-182                                                                                                                                                            ---------------------------------- Pfam domains (1)
           Pfam domains (2) -Hydrolase-1z4nB02 B:2-182                                                                                                                                                            ---------------------------------- Pfam domains (2)
         Sec.struct. author ...eeee........hhhhhhhhhhhhhhhh.......hhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhh....------------.eee.....hhhhhhhhh.......ee............hhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh.eeeee.hhhhhh...eee.hhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z4n B   1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGI------------KIALASASKNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSHYTLEFLKEVW 216
                                    10        20        30        40        50        60        70        80        90     |   -       110       120       130       140       150       160       170       180       190       200       210      
                                                                                                                          96          109
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 1z4o 1zol 2wf5 2wf6 2wf7 2wf8 2wf9 2wfa 2whe 3fm9 3zi4 4c4r 4c4s 4c4t

(-) Related Entries Specified in the PDB File

1z4o STRUCTURE OF SAME PROTEIN WITH INHIBITOR BOUND ALPHA- GALACTOSE 1-PHOSPHATE