2WF9 - JenaLib

Title :   STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE INHIBITED WITH GLUCOSE-6-PHOSPHATE, AND BERYLLIUM TRIFLUORIDE, CRYSTAL FORM 2

Authors :   M. W. Bowler, N. J. Baxter, C. E. Webster, S. Pollard, T. Alizadeh, A. M. H 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 :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   Ground State Analogue, Transition State Analogue, Isomerase, Phosphotransferase, 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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:8 , ASP A:10 , ASP A:170 , BEF A:1225 , HOH A:2006 , HOH A:2195	BINDING SITE FOR RESIDUE MG A1222
2	AC2	SOFTWARE	HOH A:2027 , HOH A:2107 , HOH A:2110 , HOH A:2114 , HOH A:2116	BINDING SITE FOR RESIDUE NA A1226
3	AC3	SOFTWARE	ASP A:10 , HIS A:20 , LEU A:44 , GLY A:46 , VAL A:47 , ARG A:49 , ALA A:115 , SER A:116 , LYS A:117 , ASN A:118 , BEF A:1225 , HOH A:2147 , HOH A:2254 , HOH A:2255 , HOH A:2256	BINDING SITE FOR RESIDUE G6P A1223
4	AC4	SOFTWARE	ASP A:10 , HIS A:20 , LEU A:44 , GLY A:46 , VAL A:47 , ARG A:49 , ALA A:115 , SER A:116 , LYS A:117 , ASN A:118 , BEF A:1225 , HOH A:2147 , HOH A:2254 , HOH A:2255 , HOH A:2256	BINDING SITE FOR RESIDUE BG6 A1224
5	AC5	SOFTWARE	ASP A:8 , LEU A:9 , ASP A:10 , SER A:114 , ALA A:115 , LYS A:145 , MG A:1222 , G6P A:1223 , BG6 A:1224 , HOH A:2006 , HOH A:2055 , HOH A:2195	BINDING SITE FOR RESIDUE BEF A1225

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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
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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 d2wf9a_ A: beta-Phosphoglucomutase                                                                                                                                                                                            SCOP domains
               CATH domains 2wf9A01       2wf9A02 A:15-92 Putative phosphatase; domain 2                                2wf9A01 A:1-14,A:93-221  [code=3.40.50.1000, no name defined]                                                                     CATH domains
               Pfam domains -Hydrolase-2wf9A01 A:2-182                                                                                                                                                            --------------------------------------- Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeee.....hhhhhhhhh.hhhhh.ee.hhhhh......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.hhhhh....eee.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wf9 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)

CATH Domains (2, 2)

Pfam Domains (1, 1)

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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	Cis Peptide Bonds
		Ala A:142 - Ala A:143	[ RasMol ]
		Ala A:60 - Asp A:61	[ RasMol ]
		Lys A:145 - Pro A:146	[ RasMol ]

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

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
2wfa	STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE INHIBITED WITH BERYLLIUM TRIFLUORIDE, IN AN OPEN CONFORMATION.

Description