EzCatDB: S00247

DB codeS00247
CATH domainDomain 13.20.70.20Catalytic domain
E.C.2.3.1.54
CSA2pfl
MACiEM0030

CATH domainRelated DB codes (homologues)
3.20.70.20M00203

Enzyme Name
Swiss-protKEGG

P09373
Protein nameFormate acetyltransferase 1formate C-acetyltransferase
pyruvate formate-lyase
pyruvic formate-lyase
formate acetyltransferase
SynonymsEC 2.3.1.54
Pyruvate formate-lyase 1

KEGG pathways
MAP codePathways
MAP00620Pyruvate metabolism
MAP00640Propanoate metabolism
MAP00650Butanoate metabolism

Swiss-prot:Accession NumberP09373
Entry namePFLB_ECOLI
ActivityAcetyl-CoA + formate = CoA + pyruvate.
SubunitHomodimer.
Subcellular locationCytoplasm.
Cofactor


SubstratesProducts
KEGG-idC00024C00058C00010C00022
CompoundAcetyl-CoAFormateCoAPyruvate
Typeamine group,carbohydrate,nucleotide,peptide/protein,sulfide groupcarboxyl groupamine group,carbohydrate,nucleotide,peptide/protein,sulfhydryl groupcarbohydrate,carboxyl group
1cm5AUnboundAnalogue:CO3UnboundUnbound
1cm5BUnboundAnalogue:CO3UnboundUnbound
1h16AUnboundUnboundBound:COABound:PYR
1h17AUnboundUnboundBound:COAAnalogue:OXM
1h18AUnboundUnboundUnboundBound:PYR
1h18BUnboundUnboundUnboundBound:PYR
1mzoAUnboundUnboundUnboundBound:PYR
1mzoBUnboundUnboundUnboundBound:PYR
1qhmAUnboundUnboundUnboundUnbound
1qhmBUnboundUnboundUnboundUnbound
2pflAUnboundUnboundUnboundUnbound
2pflBUnboundUnboundUnboundUnbound
3pflAUnboundUnboundUnboundAnalogue:OXM
3pflBUnboundUnboundUnboundAnalogue:OXM

Active-site residues
resource
Swiss-prot;P09373 & PDB;1cm5, 1h16, 1h17, 1h18, 2pfl
pdbCatalytic residuesMain-chain involved in catalysiscomment
1cm5A        ;        
GLY  734
mutant C418A, C419A
1cm5B        ;        
GLY  734
mutant C418A, C419A
1h16ACYS  418;CYS  419
GLY  734

1h17ACYS  418;CYS  419
GLY  734

1h18ACYS  418;CYS  419
GLY  734

1h18BCYS  418;CYS  419
GLY  734

1mzoACYS  418;CYS  419
GLY  734

1mzoBCYS  418;CYS  419
GLY  734

1qhmACYS 1418;CYS 1419
        
deletion 1616-1759
1qhmBCYS 2418;CYS 2419
        
deletion 2616-2759
2pflACYS  418;CYS  419
GLY  734

2pflBCYS  418;CYS  419
GLY  734

3pflACYS  418;CYS  419
GLY  734

3pflBCYS  418;CYS  419
GLY  734


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Scheme 5, p.124-125
[5]Scheme 2, Scheme 3, p.449-450
[6]Scheme 2, p.727-728
[8]Fig.7, p.999-1000
[10]p.12434-12436
[11]Scheme 1, p.5715-5717
[12]Scheme 2, Scheme 3, Scheme 4, p.2395-2398
[13]Fig.6, p.355-359
[15]Fig.1
[16]Scheme 10, Scheme 11, p.724-276
[17]Scheme 2, Scheme 3, p.11451-11455
[19]Fig.8, p.971-974
[20]Fig.4, p.R258-R261
[21]Fig.1, p.738-741
[22]Fig.4, p.48
[24]p.19-21
[28]p.2210-2211

references
[1]
PubMed ID6364987
JournalArch Biochem Biophys
Year1984
Volume228
Pages133-42
AuthorsConradt H, Hohmann-Berger M, Hohmann HP, Blaschkowski HP, Knappe J
TitlePyruvate formate-lyase (inactive form) and pyruvate formate-lyase activating enzyme of Escherichia coli
[2]
PubMed ID6369325
JournalProc Natl Acad Sci U S A
Year1984
Volume81
Pages1332-5
AuthorsKnappe J, Neugebauer FA, Blaschkowski HP, Ganzler M
TitlePost-translational activation introduces a free radical into pyruvate formate-lyase
[3]
PubMed ID3965391
JournalInfect Immun
Year1985
Volume47
Pages129-34
AuthorsYamada T, Takahashi-Abbe S, Abbe K
TitleEffects of oxygen on pyruvate formate-lyase in situ and sugar metabolism of Streptococcus mutans and Streptococcus sanguis
[4]
PubMed ID3076439
JournalBiofactors
Year1988
Volume1
Pages123-8
AuthorsKozarich JW
TitleS-adenosylmethionine-dependent enzyme activation
[5]
PubMed ID3061816
JournalEur J Biochem
Year1988
Volume178
Pages445-50
AuthorsPlaga W, Frank R, Knappe J
TitleCatalytic-site mapping of pyruvate formate lyase. Hypophosphite reaction on the acetyl-enzyme intermediate affords carbon-phosphorus bond synthesis (1-hydroxyethylphosphonate)
[6]
PubMed ID2553398
JournalEur J Biochem
Year1989
Volume184
Pages723-8
AuthorsUnkrig V, Neugebauer FA, Knappe J
TitleThe free radical of pyruvate formate-lyase. Characterization by EPR spectroscopy and involvement in catalysis as studied with the substrate-analogue hypophosphite
[7]
PubMed ID2549003
JournalJ Bacteriol
Year1989
Volume171
Pages4900-5
AuthorsWong KK, Suen KL, Kwan HS
TitleTranscription of pfl is regulated by anaerobiosis, catabolite repression, pyruvate, and oxrA: Mu dA operon fusions of Salmonella typhimurium
[8]
CommentsX-ray crystallography
PubMed ID1310545
JournalProc Natl Acad Sci U S A
Year1992
Volume89
Pages996-1000
AuthorsWagner AF, Frey M, Neugebauer FA, Schafer W, Knappe J
TitleThe free radical in pyruvate formate-lyase is located on glycine-734
Related PDB1cm5
[9]
PubMed ID8260492
JournalBiochemistry
Year1993
Volume32
Pages14102-10
AuthorsWong KK, Murray BW, Lewisch SA, Baxter MK, Ridky TW, Ulissi-DeMario L, Kozarich JW
TitleMolecular properties of pyruvate formate-lyase activating enzyme
[10]
PubMed ID8175649
JournalJ Biol Chem
Year1994
Volume269
Pages12432-7
AuthorsFrey M, Rothe M, Wagner AF, Knappe J
TitleAdenosylmethionine-dependent synthesis of the glycyl radical in pyruvate formate-lyase by abstraction of the glycine C-2 pro-S hydrogen atom. Studies of [2H]glycine-substituted enzyme and peptides homologous to the glycine 734 site.
[11]
PubMed ID7727431
JournalBiochemistry
Year1995
Volume34
Pages5712-7
AuthorsParast CV, Wong KK, Kozarich JW, Peisach J, Magliozzo RS
TitleElectron paramagnetic resonance evidence for a cysteine-based radical in pyruvate formate-lyase inactivated with mercaptopyruvate.
[12]
PubMed ID7873518
JournalBiochemistry
Year1995
Volume34
Pages2393-9
AuthorsParast CV, Wong KK, Lewisch SA, Kozarich JW, Peisach J, Magliozzo RS
TitleHydrogen exchange of the glycyl radical of pyruvate formate-lyase is catalyzed by cysteine 419.
[13]
PubMed ID8524160
JournalMethods Enzymol
Year1995
Volume258
Pages343-62
AuthorsKnappe J, Wagner AF
TitleGlycyl free radical in pyruvate formate-lyase: synthesis, structure characteristics, and involvement in catalysis.
[14]
PubMed ID9425077
JournalBiochemistry
Year1998
Volume37
Pages558-63
AuthorsReddy SG, Wong KK, Parast CV, Peisach J, Magliozzo RS, Kozarich JW
TitleDioxygen inactivation of pyruvate formate-lyase: EPR evidence for the formation of protein-based sulfinyl and peroxyl radicals.
[15]
PubMed ID9767563
JournalMol Microbiol
Year1998
Volume29
Pages945-54
AuthorsSawers G, Watson G
TitleA glycyl radical solution: oxygen-dependent interconversion of pyruvate formate-lyase.
[16]
PubMed ID11848913
JournalChem Rev
Year1998
Volume98
Pages705-762
AuthorsStubbe J, van Der Donk WA
TitleProtein Radicals in Enzyme Catalysis.
[17]
JournalJ Am Chem Soc
Year1998
Volume120
Pages11449-55
AuthorsHimo F, Eriksson LA
TitleCatalytic mechanism of pyruvate formate-lyase (PFL). A theoretical study
[18]
PubMed ID10089368
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages531-3
AuthorsLeppanen VM, Parast CV, Wong KK, Kozarich JW, Goldman A
TitlePurification and crystallization of a proteolytic fragment of Escherichia coli pyruvate formate-lyase
[19]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID99436526
PubMed ID10504733
JournalNat Struct Biol
Year1999
Volume6
Pages969-75
AuthorsBecker A, Fritz-Wolf K, Kabsch W, Knappe J, Schultz S, Volker Wagner AF
TitleStructure and mechanism of the glycyl radical enzyme pyruvate formate-lyase
Related PDB2pfl,3pfl
Related Swiss-protP09373
[20]
PubMed ID10574800
JournalStructure Fold Des
Year1999
Volume7
PagesR257-62
AuthorsEklund H, Fontecave M
TitleGlycyl radical enzymes: a conservative structural basis for radicals.
[21]
CommentsX-ray crystallography
PubMed ID10425676
JournalStructure Fold Des
Year1999
Volume7
Pages733-44
AuthorsLeppanen VM, Merckel MC, Ollis DL, Wong KK, Kozarich JW, Goldman A
TitlePyruvate formate lyase is structurally homologous to type I ribonucleotide reductase
Related PDB1qhm
[22]
PubMed ID10648809
JournalFEBS Lett
Year2000
Volume466
Pages45-8
AuthorsPlaga W, Vielhaber G, Wallach J, Knappe J
TitleModification of Cys-418 of pyruvate formate-lyase by methacrylic acid, based on its radical mechanism
[23]
PubMed ID11154425
JournalOral Microbiol Immunol
Year2000
Volume15
Pages325-8
AuthorsIwami Y, Takahashi-Abbe S, Takahashi N, Abbe K, Yamada T
TitleRate-limiting steps of glucose and sorbitol metabolism in Streptococcus mutans cells exposed to air
[24]
PubMed ID11665486
JournalAdv Protein Chem
Year2001
Volume58
Pages1-45
AuthorsFrey PA, Booker SJ
TitleRadical mechanisms of S-adenosylmethionine-dependent enzymes
[25]
PubMed ID11444864
JournalBiochem Biophys Res Commun
Year2001
Volume285
Pages456-62
AuthorsWagner AF, Schultz S, Bomke J, Pils T, Lehmann WD, Knappe J
TitleYfiD of Escherichia coli and Y06I of bacteriophage T4 as autonomous glycyl radical cofactors reconstituting the catalytic center of oxygen-fragmented pyruvate formate-lyase.
[26]
PubMed ID11300793
JournalBiochemistry
Year2001
Volume40
Pages4123-30
AuthorsZhang W, Wong KK, Magliozzo RS, Kozarich JW
TitleInactivation of pyruvate formate-lyase by dioxygen
[27]
PubMed ID11278506
JournalJ Biol Chem
Year2001
Volume276
Pages12924-7
AuthorsKrieger CJ, Roseboom W, Albracht SP, Spormann AM
TitleA stable organic free radical in anaerobic benzylsuccinate synthase of Azoarcus sp. strain T
[28]
CommentsX-ray crystallography
PubMed ID12454503
JournalActa Crystallogr D Biol Crystallogr
Year2002
Volume58
Pages2209-12
AuthorsLehtio L, Leppanen VM, Kozarich JW, Goldman A
TitleStructure of Escherichia coli pyruvate formate-lyase with pyruvate.
Related PDB1mzo
[29]
PubMed ID12236732
JournalJ Am Chem Soc
Year2002
Volume124
Pages11270-1
AuthorsWalsby CJ, Ortillo D, Broderick WE, Broderick JB, Hoffman BM
TitleAn anchoring role for FeS clusters: chelation of the amino acid moiety of S-adenosylmethionine to the unique iron site of the [4Fe-4S] cluster of pyruvate formate-lyase activating enzyme.
[30]
CommentsX-ray crystallography
PubMed ID12163496
JournalJ Biol Chem
Year2002
Volume277
Pages40036-42
AuthorsBecker A, Kabsch W
TitleX-ray structure of pyruvate formate-lyase in complex with pyruvate and CoA. How the enzyme uses the Cys-418 thiyl radical for pyruvate cleavage.
Related PDB1h16,1h17,1h18

comments
This enzyme catalyzes radical reactions, instead of an ordinary transfer reaction.

createdupdated
2005-03-302009-02-26


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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