EzCatDB: S00366
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DB codeS00366
RLCP classification3.100.220195.81 : Transfer
CATH domainDomain 13.40.50.1240 : Rossmann foldCatalytic domain
E.C.5.4.2.1
CSA1qhf

CATH domainRelated DB codes (homologues)
3.40.50.1240 : Rossmann foldS00365,S00363,D00460,D00514

Enzyme Name
UniProtKBKEGG

P62707P0A5R6Q6MWZ7P00950P36623
Protein name2,3-bisphosphoglycerate-dependent phosphoglycerate mutase2,3-bisphosphoglycerate-dependent phosphoglycerate mutase(Possible phosphoglycerate mutase Gpm2Phosphoglycerate mutase 1Phosphoglycerate mutasephosphoglycerate mutase
phosphoglycerate phosphomutase
phosphoglyceromutase
glycerate phosphomutase (diphosphoglycerate cofactor)
monophosphoglycerate mutase
monophosphoglyceromutase
diphosphoglycomutase
diphosphoglycerate mutase
bisphosphoglyceromutase
GriP mutase
MPGM
PGA mutase
PGAM-i
PGAM
PGAM-d
PGM
SynonymsBPG-dependent PGAM
PGAM
Phosphoglyceromutase
dPGM
EC 5.4.2.1
BPG-dependent PGAM
PGAM
Phosphoglyceromutase
dPGM
EC 5.4.2.1
Phosphoglyceromutase
PGAM) (BPG-dependent PGAM)
PGAM 1
EC 5.4.2.1
BPG-dependent PGAM 1
MPGM 1
Phosphoglyceromutase 1
PGAM
EC 5.4.2.1
BPG-dependent PGAM
MPGM
Phosphoglyceromutase
RefSeqNP_415276.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489028.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_334917.1 (Protein)
NC_002755.2 (DNA/RNA sequence)
YP_006513819.1 (Protein)
NC_018143.1 (DNA/RNA sequence)
YP_177731.1 (Protein)
NC_000962.3 (DNA/RNA sequence)
YP_006516686.1 (Protein)
NC_018143.1 (DNA/RNA sequence)
YP_177944.1 (Protein)
NC_000962.3 (DNA/RNA sequence)
NP_012770.1 (Protein)
NM_001179718.1 (DNA/RNA sequence)
NP_594889.1 (Protein)
NM_001020318.2 (DNA/RNA sequence)
PfamPF00300 (His_Phos_1)
[Graphical view]
PF00300 (His_Phos_1)
[Graphical view]
PF00300 (His_Phos_1)
[Graphical view]
PF00300 (His_Phos_1)
[Graphical view]
PF00300 (His_Phos_1)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00010Glycolysis / Gluconeogenesis

UniProtKB:Accession NumberP62707P0A5R6Q6MWZ7P00950P36623
Entry nameGPMA_ECOLIGPMA_MYCTUQ6MWZ7_MYCTUPMG1_YEASTPMGY_SCHPO
Activity2-phospho-D-glycerate = 3-phospho-D-glycerate.2-phospho-D-glycerate = 3-phospho-D-glycerate.
2-phospho-D-glycerate = 3-phospho-D-glycerate.2-phospho-D-glycerate = 3-phospho-D-glycerate.
SubunitHomodimer.

Homotetramer.Monomer.
Subcellular location




Cofactor





Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC01159C00631C00197C04262
Compound2,3-Bisphospho-D-glycerate2-Phospho-D-glycerate3-Phospho-D-glycerateProtein N(tau)-phospho-L-histidine
Typecarboxyl group,phosphate group/phosphate ioncarbohydrate,carboxyl group,phosphate group/phosphate ioncarbohydrate,carboxyl group,phosphate group/phosphate ion
ChEBI17720
17835
17794

PubChem186004
439278
439183

            
1e58AUnboundUnboundUnboundIntermediate-bound:HIS 10-NEP
1e59AAnalogue:VO3UnboundUnboundUnbound
1riiAUnboundAnalogue:GOLUnboundUnbound
1riiBUnboundAnalogue:GOLUnboundUnbound
1riiCUnboundUnboundUnboundUnbound
1riiDUnboundAnalogue:GOLUnboundUnbound
2a6pAUnboundAnalogue:GOL-SO4UnboundUnbound
2a6pBUnboundAnalogue:GOL-SO4UnboundUnbound
1bq3AAnalogue:IHPUnboundUnboundUnbound
1bq3BUnboundUnboundUnboundUnbound
1bq3CUnboundUnboundUnboundUnbound
1bq3DAnalogue:IHPUnboundUnboundUnbound
1bq4AUnboundUnboundUnboundUnbound
1bq4BUnboundUnboundUnboundUnbound
1bq4CUnboundUnboundUnboundUnbound
1bq4DUnboundUnboundUnboundUnbound
1qhfAUnboundUnboundBound:3PGUnbound
1qhfBUnboundUnboundBound:3PGUnbound
3pgmAUnboundUnboundBound:3PGUnbound
4pgmAUnboundUnboundUnboundUnbound
4pgmBUnboundUnboundUnboundUnbound
4pgmCUnboundUnboundUnboundUnbound
4pgmDUnboundUnboundUnboundUnbound
5pgmAUnboundUnboundUnboundUnbound
5pgmBUnboundUnboundUnboundUnbound
5pgmCUnboundUnboundUnboundUnbound
5pgmDUnboundUnboundUnboundUnbound
5pgmEUnboundUnboundUnboundUnbound
5pgmFUnboundUnboundUnboundUnbound
5pgmGUnboundUnboundUnboundUnbound
5pgmHUnboundUnboundUnboundUnbound
1fztAUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P00950, P62707, P36623 & literature [18]
pdbCatalytic residuesModified residuescomment
           
1e58AHIS 10;GLU 88;ARG  9;ASN 16;ARG 61;HIS 183
HIS 10(Phosphorylation)
Modified residue H10-NEP
1e59AHIS 10;GLU 88;ARG  9;ASN 16;ARG 61;HIS 183
HIS 10(Phosphorylation)
 
1riiAHIS 12;GLU 90;ARG 11;ASN 18;ARG 63;HIS 183
HIS 12(Phosphorylation)
 
1riiBHIS 12;GLU 90;ARG 11;ASN 18;ARG 63;HIS 183
HIS 12(Phosphorylation)
 
1riiCHIS 12;GLU 90;ARG 11;ASN 18;ARG 63;HIS 183
HIS 12(Phosphorylation)
 
1riiDHIS 12;GLU 90;ARG 11;ASN 18;ARG 63;HIS 183
HIS 12(Phosphorylation)
 
2a6pAHIS 13;GLU 85;ARG 12;      ;ARG 64;HIS 147
HIS 13(Phosphorylation)
 
2a6pBHIS 13;GLU 85;ARG 12;      ;ARG 64;HIS 147
HIS 13(Phosphorylation)
 
1bq3AHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
1bq3BHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
1bq3CHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
1bq3DHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
1bq4AHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
1bq4BHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
1bq4CHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
1bq4DHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
1qhfAHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
1qhfBHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
3pgmAHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 179
HIS  8(Phosphorylation)
 
4pgmAHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
4pgmBHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
4pgmCHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
4pgmDHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
5pgmAHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
5pgmBHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
5pgmCHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
5pgmDHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
5pgmEHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
5pgmFHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
5pgmGHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
5pgmHHIS  8;GLU 86;ARG  7;ASN 14;ARG 59;HIS 181
HIS  8(Phosphorylation)
 
1fztAHIS 15;GLU 93;ARG 14;ASN 21;ARG 66;HIS 163
HIS 15(Phosphorylation)
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Scheme II, p.741-742
[4]Fig.3, p.125-128
[14]p.455-457
[15]p.1825-1826
[18]Fig.5, p.1511-1515
[23]p.1076-1077
[24]p.1133-1137
[26]p.82-83

references
[1]
PubMed ID6251799
JournalBiochem Biophys Res Commun
Year1980
Volume95
Pages132-9
AuthorsHass LF, Miller KB
TitleHuman erythrocyte phosphoglycerate mutase: evidence for normal catalysis in the absence of added 2,3-bisphospho-D-glycerate.
[2]
PubMed ID6243955
JournalBiochemistry
Year1980
Volume19
Pages738-43
AuthorsBlattler WA, Knowles JR
TitlePhosphoglycerate mutases: stereochemical course of the phosphoryl group transfers catalyzed by the cofactor-dependent enzyme from rabbit muscle and the cofactor-independent enzyme from wheat germ.
[3]
PubMed ID6115417
JournalPhilos Trans R Soc Lond B Biol Sci
Year1981
Volume293
Pages177-89
AuthorsSternberg MJ, Cohen FE, Taylor WR, Feldmann RJ
TitleAnalysis and predication of structural motifs in the glycolytic enzymes.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
Medline ID81273329
PubMed ID6115412
JournalPhilos Trans R Soc Lond B Biol Sci
Year1981
Volume293
Pages121-30
AuthorsWinn SI, Watson HC, Harkins RN, Fothergill LA
TitleStructure and activity of phosphoglycerate mutase.
Related PDB3pgm
Related UniProtKBP00950
[5]
PubMed ID6282653
JournalFed Proc
Year1982
Volume41
Pages2424-31
AuthorsKnowles JR
TitlePhospho transfer enzymes: lessons from stereochemistry.
[6]
PubMed ID6318807
JournalBiochemistry
Year1983
Volume22
Pages6130-4
AuthorsHunt AG, Simplaceanu V, Hong JS, Ho C
TitlePhosphorus-31 nuclear magnetic resonance investigation of membrane vesicles from Escherichia coli.
[7]
PubMed ID6331428
JournalBiochem Biophys Res Commun
Year1984
Volume121
Pages826-33
AuthorsAmato SV, Rose ZB, Liebman MN
TitleMacro-structural organization of phosphoglycerate mutase.
[8]
PubMed ID6331429
JournalBiochem Biophys Res Commun
Year1984
Volume121
Pages834-41
AuthorsRose ZB, Kaklij GS
TitleThe effects of anions on phosphoglycerate mutase.
[9]
PubMed ID1659318
JournalArch Biochem Biophys
Year1991
Volume291
Pages201-11
AuthorsMendz GL
TitleStimulation of mutases and isomerases by vanadium.
[10]
PubMed ID8110200
JournalBiochem J
Year1994
Volume297
Pages603-8
AuthorsNairn J, Price NC, Fothergill-Gilmore LA, Walker GE, Fothergill JE, Dunbar B
TitleThe amino acid sequence of the small monomeric phosphoglycerate mutase from the fission yeast Schizosaccharomyces pombe.
[11]
PubMed ID8765231
JournalBiochim Biophys Acta
Year1996
Volume1296
Pages69-75
AuthorsNairn J, Price NC, Kelly SM, Rigden D, Fothergill-Gilmore LA, Krell T
TitlePhosphoglycerate mutase from Schizosaccharomyces pombe: development of an expression system and characterisation of three histidine mutants of the enzyme.
[12]
PubMed ID9030753
JournalEur J Biochem
Year1997
Volume243
Pages306-14
AuthorsSeip S, Lanz R, Gutknecht R, Flukiger K, Erni B
TitleThe fructose transporter of Bacillus subtilis encoded by the lev operon: backbone assignment and secondary structure of the IIB(Lev) subunit.
[13]
PubMed ID9390410
JournalJ Biomol NMR
Year1997
Volume10
Pages309-10
AuthorsUhrinova S, Uhrin D, Nairn J, Price NC, Fothergill-Gilmore LA, Barlow PN
TitleBackbone assignment of double labelled 23.7 kDa phosphoglycerate mutase from Schizosaccharomyces pombe.
[14]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID98173871
PubMed ID9512715
JournalJ Mol Biol
Year1998
Volume276
Pages449-59
AuthorsRigden DJ, Alexeev D, Phillips SE, Fothergill-Gilmore LA
TitleThe 2.3 A X-ray crystal structure of S. cerevisiae phosphoglycerate mutase.
Related PDB4pgm
Related UniProtKBP00950
[15]
CommentsX-ray crystallography
PubMed ID10531478
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages1822-6
AuthorsCrowhurst GS, Dalby AR, Isupov MN, Campbell JW, Littlechild JA
TitleStructure of a phosphoglycerate mutase:3-phosphoglyceric acid complex at 1.7 A.
Related PDB1qhf
[16]
PubMed ID10437801
JournalFEBS Lett
Year1999
Volume455
Pages344-8
AuthorsFraser HI, Kvaratskhelia M, White MF
TitleThe two analogous phosphoglycerate mutases of Escherichia coli.
[17]
CommentsX-ray crystallography
PubMed ID10369755
JournalJ Mol Biol
Year1999
Volume289
Pages691-9
AuthorsRigden DJ, Walter RA, Phillips SE, Fothergill-Gilmore LA
TitlePolyanionic inhibitors of phosphoglycerate mutase: combined structural and biochemical analysis.
Related PDB1bq3,1bq4
[18]
CommentsX-ray crystallography
PubMed ID10064712
JournalJ Mol Biol
Year1999
Volume286
Pages1507-17
AuthorsRigden DJ, Walter RA, Phillips SE, Fothergill-Gilmore LA
TitleSulphate ions observed in the 2.12 A structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism.
Related PDB5pgm
[19]
PubMed ID11106417
JournalEur J Biochem
Year2000
Volume267
Pages7065-74
AuthorsNairn J, Duncan D, Price NE, Kelly SM, Fothergill-Gilmore LA, Uhrinova S, Barlow PN, Rigden DJ, Price NC
TitleCharacterization of active-site mutants of Schizosaccharomyces pombe phosphoglycerate mutase. Elucidation of the roles of amino acids involved in substrate binding and catalysis.
[20]
CommentsX-ray crystallography
PubMed ID11038361
JournalJ Biol Chem
Year2001
Volume276
Pages3247-53
AuthorsBond CS, White MF, Hunter WN
TitleHigh resolution structure of the phosphohistidine-activated form of Escherichia coli cofactor-dependent phosphoglycerate mutase.
Related PDB1e58
Related UniProtKBP62707
[21]
CommentsNMR, 21 STRUCTURES
PubMed ID11237600
JournalJ Mol Biol
Year2001
Volume306
Pages275-90
AuthorsUhrinova S, Uhrin D, Nairn J, Price NC, Fothergill-Gilmore LA, Barlow PN
TitleSolution structure and dynamics of an open beta-sheet, glycolytic enzyme, monomeric 23.7 kDa phosphoglycerate mutase from Schizosaccharomyces pombe.
Related PDB1fzt
[22]
PubMed ID11514674
JournalProtein Sci
Year2001
Volume10
Pages1835-46
AuthorsRigden DJ, Bagyan I, Lamani E, Setlow P, Jedrzejas MJ
TitleA cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus is actually a broad specificity phosphatase.
[23]
CommentsX-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS).
PubMed ID11884145
JournalJ Mol Biol
Year2002
Volume316
Pages1071-81
AuthorsBond CS, White MF, Hunter WN
TitleMechanistic implications for Escherichia coli cofactor-dependent phosphoglycerate mutase based on the high-resolution crystal structure of a vanadate complex.
Related PDB1e59
Related UniProtKBP62707
[24]
PubMed ID11827481
JournalJ Mol Biol
Year2002
Volume315
Pages1129-43
AuthorsRigden DJ, Mello LV, Setlow P, Jedrzejas MJ
TitleStructure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity.
[25]
PubMed ID11951058
JournalMed Sci Monit
Year2002
Volume8
PagesBR123-35
AuthorsTorshin IY
TitleFunctional maps of the junctions between interglobular contacts and active sites in glycolytic enzymes -- a comparative analysis of the biochemical and structural data.
[26]
PubMed ID12586342
JournalFEBS Lett
Year2003
Volume536
Pages77-84
AuthorsRigden DJ
TitleUnexpected catalytic site variation in phosphoprotein phosphatase homologues of cofactor-dependent phosphoglycerate mutase.
[27]
PubMed ID15258155
JournalJ Biol Chem
Year2004
Volume279
Pages39132-8
AuthorsWang Y, Wei Z, Bian Q, Cheng Z, Wan M, Liu L, Gong W
TitleCrystal structure of human bisphosphoglycerate mutase.
[28]
PubMed ID15735341
JournalActa Crystallogr D Biol Crystallogr
Year2005
Volume61
Pages309-15
AuthorsMuller P, Sawaya MR, Pashkov I, Chan S, Nguyen C, Wu Y, Perry LJ, Eisenberg D
TitleThe 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase.
Related PDB1rii
[29]
PubMed ID16672613
JournalJ Bacteriol
Year2006
Volume188
Pages3589-99
AuthorsWatkins HA, Baker EN
TitleStructural and functional analysis of Rv3214 from Mycobacterium tuberculosis, a protein with conflicting functional annotations, leads to its characterization as a phosphatase.
Related PDB2a6p

comments
This enzyme is homologous to a phosphatase (E.C. 3.1.3.46; S00365 in EzCatDB).
This enzyme catalyzes a kind of intermolecular transfer reaction, which comprises the following steps of the reaction in the double-displacement mechanism.
(a) 2,3-BPG (cofactor) + enzyme => 3-PGA (or 2-PGA) (product) + phosphorylated enzyme
(b) 2-PGA (or 3-PGA) (substrate) + phosphorylated enzyme => 2,3-BPG (cofactor) + enzyme
Accoding to the literature [14], [18], [23], [24] & [26], the reaction mechanism of this enzyme seems to be as follows:
(a) 2,3-BPG (cofactor) + enzyme => 3-PGA (or 2-PGA) (product) + phosphorylated enzyme
(1) Arg59 and His181 modulate the nucleophilicity of His8, keeping His8 unprotonated.
(2) His8 makes a nucleophilic attack on one of the phosphoryl groups of 2,3-BPG, leading to a pentacovalent transition-state.
(3) The transition state seems to be stabilized by Arg7, Asn14, Arg59 and His181, whereas Glu86 acts as a general acid to protonate the leaving hydroxyl group, probably through a water molecule.
(b) 2-PGA (or 3-PGA) (substrate) + phosphorylated enzyme => 2,3-BPG (cofactor) + enzyme
(4) Glu86 now acts as a general base to deprotonate and activate another hydroxyl group of substrate.
(5) The activated acceptor, hydroxyl group, makes a nucleophilic attack on the phosphoryl group on His8, leading to a transition state.
(6) The transition state seems to be stabilized by Arg7, Asn14, Arg59 and His181.

createdupdated
2005-06-142015-10-27


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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