EzCatDB: S00242

DB codeS00242
CATH domainDomain 13.20.20.60Catalytic domain
E.C.5.4.2.9
CSA1pym
MACiEM0271

CATH domainRelated DB codes (homologues)
3.20.20.60S00241,T00217,S00197,T00043,D00477

Enzyme Name
Swiss-protKEGG

P56839
Protein namePhosphoenolpyruvate phosphomutasephosphoenolpyruvate mutase
phosphoenolpyruvate-phosphonopyruvate phosphomutase
PEP phosphomutase
phosphoenolpyruvate phosphomutase
PEPPM
PEP phosphomutase
SynonymsPEP phosphomutase
Phosphoenolpyruvate mutase
PEP mutase
EC 5.4.2.9

KEGG pathways
MAP codePathways
MAP00440Aminophosphonate metabolism

Swiss-prot:Accession NumberP56839
Entry namePEPM_MYTED
ActivityPhosphoenolpyruvate = 3-phosphonopyruvate.
SubunitHomotetramer.
Subcellular location
CofactorMagnesium.


CofactorsSubstratesProductsintermediates
KEGG-idC00305C00074C02798I00001I00002
CompoundMagnesiumPhosphoenolpyruvate3-PhosphonopyruvatePyruvate enolateMetaphosphate
Typedivalent metal (Ca2+, Mg2+)carboxyl group,phosphate group/phosphate ioncarbohydrate,carboxyl group,phosphate group/phosphate ion

1m1bABound:_MGUnboundAnalogue:SPVUnboundUnbound
1m1bBBound:_MGUnboundAnalogue:SPVUnboundUnbound
1pymABound:_MGUnboundUnboundIntermediate-analogue:OXLUnbound
1pymBBound:_MGUnboundUnboundIntermediate-analogue:OXLUnbound
1s2tAUnboundUnboundUnboundUnboundUnbound
1s2tBUnboundUnboundUnboundUnboundUnbound
1s2uAUnboundUnboundUnboundUnboundUnbound
1s2uBUnboundUnboundUnboundUnboundUnbound
1s2vABound:_MGUnboundUnboundUnboundUnbound
1s2vBBound:_MGUnboundUnboundUnboundUnbound
1s2vCBound:_MGUnboundUnboundUnboundUnbound
1s2vDBound:_MGUnboundUnboundUnboundUnbound
1s2wAUnboundUnboundUnboundUnboundTransition-state-analogue:SO4

Active-site residues
resource
literature [9], [12]
pdbCatalytic residuesCofactor-binding residuescomment
1m1bAARG 159;HIS 190;ASN 122
ASP 85(Magnesium binding)

1m1bBARG 159;HIS 190;ASN 122
ASP 85(Magnesium binding)

1pymAARG 159;HIS 190;ASN 122
ASP 85(Magnesium binding)

1pymBARG 159;HIS 190;ASN 122
ASP 85(Magnesium binding)

1s2tAARG 159;HIS 190;ASN 122
ASP 85(Magnesium binding)

1s2tBARG 159;HIS 190;ASN 122
ASP 85(Magnesium binding)

1s2uAARG 159;HIS 190;ASN 122
ASP 85(Magnesium binding)
mutant D58A
1s2uBARG 159;HIS 190;ASN 122
ASP 85(Magnesium binding)
mutant D58A
1s2vAARG 159;HIS 190;ASN 122
ASP 85(Magnesium binding)
invisible 123-129
1s2vBARG 159;HIS 190;ASN 122
ASP 85(Magnesium binding)
invisible 124-126
1s2vCARG 159;HIS 190;       
ASP 85(Magnesium binding)
invisible 121-129
1s2vDARG 159;HIS 190;       
ASP 85(Magnesium binding)
invisible 120-129
1s2wAARG 159;HIS 190;       
ASP 85(Magnesium binding)
invisible 55-63, 119-126

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.1, Fig.2, Fig.3, Fig.4, Fig.5, Fig.6
[3]Scheme 2, p.4629
[5]Scheme 2, Fig.2, p.14171-14172
[6]p.543-544
[9]Fig.5 II, p.10274-10275
[12]p.4450-4452
[13]SCHEME 1, p.13833

references
[1]
PubMed ID8180189
JournalBiochemistry
Year1994
Volume33
Pages5641-6
AuthorsSeidel HM, Knowles JR
TitleInteraction of inhibitors with phosphoenolpyruvate mutase: implications for the reaction mechanism and the nature of the active site.
[2]
PubMed ID8948453
JournalBiochem J
Year1995
Volume308
Pages931-5
AuthorsChawla S, Mutenda EK, Dixon HB, Freeman S, Smith AW
TitleSynthesis of 3-arsonopyruvate and its interaction with phosphoenolpyruvate mutase.
[3]
PubMed ID8605214
JournalBiochemistry
Year1996
Volume35
Pages4628-35
AuthorsKim J, Dunaway-Mariano D
TitlePhosphoenolpyruvate mutase catalysis of phosphoryl transfer in phosphoenolpyruvate: kinetics and mechanism of phosphorus-carbon bond formation.
[4]
PubMed ID9468496
JournalJ Biol Chem
Year1998
Volume273
Pages4443-8
AuthorsKim A, Kim J, Martin BM, Dunaway-Mariano D
TitleIsolation and characterization of the carbon-phosphorus bond-forming enzyme phosphoenolpyruvate mutase from the mollusk Mytilus edulis.
[5]
PubMed ID10571990
JournalBiochemistry
Year1999
Volume38
Pages14165-73
AuthorsJia Y, Lu Z, Huang K, Herzberg O, Dunaway-Mariano D
TitleInsight into the mechanism of phosphoenolpyruvate mutase catalysis derived from site-directed mutagenesis studies of active site residues.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS).
Medline ID99306036
PubMed ID10378273
JournalStructure Fold Des
Year1999
Volume7
Pages539-48
AuthorsHuang K, Li Z, Jia Y, Dunaway-Mariano D, Herzberg O
TitleHelix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate.
Related PDB1pym
Related Swiss-protP56839
[7]
PubMed ID10801489
JournalStructure Fold Des
Year2000
Volume8
Pages349-62
AuthorsBritton K, Langridge S, Baker PJ, Weeradechapon K, Sedelnikova SE, De Lucas JR, Rice DW, Turner G
TitleThe crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans.
[8]
PubMed ID11526312
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages1209-18
AuthorsBritton KL, Abeysinghe IS, Baker PJ, Barynin V, Diehl P, Langridge SJ, McFadden BA, Sedelnikova SE, Stillman TJ, Weeradechapon K, Rice DW
TitleThe structure and domain organization of Escherichia coli isocitrate lyase.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF 5-294 IN COMPLEX WITH SULFOPYRUVATE, AND MUTAGENESIS OF ASP-57; ASN-121 AND HIS-189.
PubMed ID12162742
JournalBiochemistry
Year2002
Volume41
Pages10270-6
AuthorsLiu S, Lu Z, Jia Y, Dunaway-Mariano D, Herzberg O
TitleDissociative phosphoryl transfer in PEP mutase catalysis: structure of the enzyme/sulfopyruvate complex and kinetic properties of mutants.
Related PDB1m1b
Related Swiss-protP56839
[10]
PubMed ID12837791
JournalJ Bacteriol
Year2003
Volume185
Pages4163-71
AuthorsSchmitzberger F, Smith AG, Abell C, Blundell TL
TitleComparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily.
[11]
PubMed ID12672809
JournalJ Biol Chem
Year2003
Volume278
Pages22703-8
AuthorsSarkar M, Hamilton CJ, Fairlamb AH
TitleProperties of phosphoenolpyruvate mutase, the first enzyme in the aminoethylphosphonate biosynthetic pathway in Trypanosoma cruzi.
[12]
PubMed ID15078090
JournalBiochemistry
Year2004
Volume43
Pages4447-53
AuthorsLiu S, Lu Z, Han Y, Jia Y, Howard A, Dunaway-Mariano D, Herzberg O
TitleConformational flexibility of PEP mutase.
Related PDB1s2t,1s2u,1s2v,1s2w
[13]
JournalJ Phys Chem B Condens Matter Mater Surf Interfaces Biophys
Year2005
Volume109
Pages13827-34
AuthorsXu DG, Guo H, Liu Y, York DM
TitleTheoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: Solvent effects, thio effects, and implications for enzymatic reactions.

comments
Although there have been two catalytic mechanism for this enzyme, associative mechanism and dissociative mechanism, the literature [9] and [12] suggested that the dissociative mechanism, in which pyruvate enolate and metaphosphate are formed during catalysis, must be more likely.
Thus, this enzyme catalyzes the following reaction (see [9], [12], [13]):
(A) Elimination of metaphosphate from PEP, forming pyruvate enolate:
(B) Addition of metaphosphate to the sp2 carbon of pyruvate enolate:

createdupdated
2004-04-072009-02-26
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 2010)
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)

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