DB code: S00247

CATH domain 3.20.70.20 : Anaerobic Ribonucleotide-triphosphate Reductase Large Chain Catalytic domain
E.C. 2.3.1.54
CSA 2pfl
M-CSA 2pfl
MACiE M0030

CATH domain Related DB codes (homologues)
3.20.70.20 : Anaerobic Ribonucleotide-triphosphate Reductase Large Chain M00203

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P09373 Formate acetyltransferase 1
EC 2.3.1.54
Pyruvate formate-lyase 1
NP_415423.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489175.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01228 (Gly_radical)
PF02901 (PFL)
[Graphical View]

KEGG enzyme name
formate C-acetyltransferase
pyruvate formate-lyase
pyruvic formate-lyase
formate acetyltransferase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P09373 PFLB_ECOLI Acetyl-CoA + formate = CoA + pyruvate. Homodimer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00620 Pyruvate metabolism
MAP00640 Propanoate metabolism
MAP00650 Butanoate metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00024 C00058 C00010 C00022
E.C.
Compound Acetyl-CoA Formate CoA Pyruvate
Type amine group,carbohydrate,nucleotide ,peptide/protein,sulfide group carboxyl group amine group,carbohydrate,nucleotide ,peptide/protein,sulfhydryl group carbohydrate,carboxyl group
ChEBI 15351
 15351
 		30751
 30751
 		15346
 15346
 		32816
 32816
PubChem 444493
 6302
 444493
 6302
 		18971002
 284
 18971002
 284
 		6816
 87642
 6816
 87642
 		1060
 1060
1cm5A Unbound Analogue:CO3 Unbound Unbound
1cm5B Unbound Analogue:CO3 Unbound Unbound
1h16A Unbound Unbound Bound:COA Bound:PYR
1h17A Unbound Unbound Bound:COA Analogue:OXM
1h18A Unbound Unbound Unbound Bound:PYR
1h18B Unbound Unbound Unbound Bound:PYR
1mzoA Unbound Unbound Unbound Bound:PYR
1mzoB Unbound Unbound Unbound Bound:PYR
1qhmA Unbound Unbound Unbound Unbound
1qhmB Unbound Unbound Unbound Unbound
2pflA Unbound Unbound Unbound Unbound
2pflB Unbound Unbound Unbound Unbound
3pflA Unbound Unbound Unbound Analogue:OXM
3pflB Unbound Unbound Unbound Analogue:OXM

Reference for Active-site residues
resource references E.C.
Swiss-prot;P09373 & PDB;1cm5, 1h16, 1h17, 1h18, 2pfl

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1cm5A ; GLY 734 mutant C418A, C419A
1cm5B ; GLY 734 mutant C418A, C419A
1h16A CYS 418;CYS 419 GLY 734
1h17A CYS 418;CYS 419 GLY 734
1h18A CYS 418;CYS 419 GLY 734
1h18B CYS 418;CYS 419 GLY 734
1mzoA CYS 418;CYS 419 GLY 734
1mzoB CYS 418;CYS 419 GLY 734
1qhmA CYS 1418;CYS 1419 deletion 1616-1759
1qhmB CYS 2418;CYS 2419 deletion 2616-2759
2pflA CYS 418;CYS 419 GLY 734
2pflB CYS 418;CYS 419 GLY 734
3pflA CYS 418;CYS 419 GLY 734
3pflB CYS 418;CYS 419 GLY 734

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 6364987
Journal Arch Biochem Biophys
Year 1984
Volume 228
Pages 133-42
Authors Conradt H, Hohmann-Berger M, Hohmann HP, Blaschkowski HP, Knappe J
Title Pyruvate formate-lyase (inactive form) and pyruvate formate-lyase activating enzyme of Escherichia coli
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6369325
Journal Proc Natl Acad Sci U S A
Year 1984
Volume 81
Pages 1332-5
Authors Knappe J, Neugebauer FA, Blaschkowski HP, Ganzler M
Title Post-translational activation introduces a free radical into pyruvate formate-lyase
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 3965391
Journal Infect Immun
Year 1985
Volume 47
Pages 129-34
Authors Yamada T, Takahashi-Abbe S, Abbe K
Title Effects of oxygen on pyruvate formate-lyase in situ and sugar metabolism of Streptococcus mutans and Streptococcus sanguis
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 3076439
Journal Biofactors
Year 1988
Volume 1
Pages 123-8
Authors Kozarich JW
Title S-adenosylmethionine-dependent enzyme activation
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 3061816
Journal Eur J Biochem
Year 1988
Volume 178
Pages 445-50
Authors Plaga W, Frank R, Knappe J
Title Catalytic-site mapping of pyruvate formate lyase. Hypophosphite reaction on the acetyl-enzyme intermediate affords carbon-phosphorus bond synthesis (1-hydroxyethylphosphonate)
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 2553398
Journal Eur J Biochem
Year 1989
Volume 184
Pages 723-8
Authors Unkrig V, Neugebauer FA, Knappe J
Title The free radical of pyruvate formate-lyase. Characterization by EPR spectroscopy and involvement in catalysis as studied with the substrate-analogue hypophosphite
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 2549003
Journal J Bacteriol
Year 1989
Volume 171
Pages 4900-5
Authors Wong KK, Suen KL, Kwan HS
Title Transcription of pfl is regulated by anaerobiosis, catabolite repression, pyruvate, and oxrA: Mu dA operon fusions of Salmonella typhimurium
Related PDB
Related UniProtKB
[8]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 1310545
Journal Proc Natl Acad Sci U S A
Year 1992
Volume 89
Pages 996-1000
Authors Wagner AF, Frey M, Neugebauer FA, Schafer W, Knappe J
Title The free radical in pyruvate formate-lyase is located on glycine-734
Related PDB 1cm5
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 8260492
Journal Biochemistry
Year 1993
Volume 32
Pages 14102-10
Authors Wong KK, Murray BW, Lewisch SA, Baxter MK, Ridky TW, Ulissi-DeMario L, Kozarich JW
Title Molecular properties of pyruvate formate-lyase activating enzyme
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 8175649
Journal J Biol Chem
Year 1994
Volume 269
Pages 12432-7
Authors Frey M, Rothe M, Wagner AF, Knappe J
Title Adenosylmethionine-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.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 7727431
Journal Biochemistry
Year 1995
Volume 34
Pages 5712-7
Authors Parast CV, Wong KK, Kozarich JW, Peisach J, Magliozzo RS
Title Electron paramagnetic resonance evidence for a cysteine-based radical in pyruvate formate-lyase inactivated with mercaptopyruvate.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 7873518
Journal Biochemistry
Year 1995
Volume 34
Pages 2393-9
Authors Parast CV, Wong KK, Lewisch SA, Kozarich JW, Peisach J, Magliozzo RS
Title Hydrogen exchange of the glycyl radical of pyruvate formate-lyase is catalyzed by cysteine 419.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 8524160
Journal Methods Enzymol
Year 1995
Volume 258
Pages 343-62
Authors Knappe J, Wagner AF
Title Glycyl free radical in pyruvate formate-lyase: synthesis, structure characteristics, and involvement in catalysis.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 9425077
Journal Biochemistry
Year 1998
Volume 37
Pages 558-63
Authors Reddy SG, Wong KK, Parast CV, Peisach J, Magliozzo RS, Kozarich JW
Title Dioxygen inactivation of pyruvate formate-lyase: EPR evidence for the formation of protein-based sulfinyl and peroxyl radicals.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 9767563
Journal Mol Microbiol
Year 1998
Volume 29
Pages 945-54
Authors Sawers G, Watson G
Title A glycyl radical solution: oxygen-dependent interconversion of pyruvate formate-lyase.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11848913
Journal Chem Rev
Year 1998
Volume 98
Pages 705-762
Authors Stubbe J, van Der Donk WA
Title Protein Radicals in Enzyme Catalysis.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID
Journal J Am Chem Soc
Year 1998
Volume 120
Pages 11449-55
Authors Himo F, Eriksson LA
Title Catalytic mechanism of pyruvate formate-lyase (PFL). A theoretical study
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 10089368
Journal Acta Crystallogr D Biol Crystallogr
Year 1999
Volume 55
Pages 531-3
Authors Leppanen VM, Parast CV, Wong KK, Kozarich JW, Goldman A
Title Purification and crystallization of a proteolytic fragment of Escherichia coli pyruvate formate-lyase
Related PDB
Related UniProtKB
[19]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 99436526
PubMed ID 10504733
Journal Nat Struct Biol
Year 1999
Volume 6
Pages 969-75
Authors Becker A, Fritz-Wolf K, Kabsch W, Knappe J, Schultz S, Volker Wagner AF
Title Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase
Related PDB 2pfl 3pfl
Related UniProtKB P09373
[20]
Resource
Comments
Medline ID
PubMed ID 10574800
Journal Structure Fold Des
Year 1999
Volume 7
Pages R257-62
Authors Eklund H, Fontecave M
Title Glycyl radical enzymes: a conservative structural basis for radicals.
Related PDB
Related UniProtKB
[21]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10425676
Journal Structure Fold Des
Year 1999
Volume 7
Pages 733-44
Authors Leppanen VM, Merckel MC, Ollis DL, Wong KK, Kozarich JW, Goldman A
Title Pyruvate formate lyase is structurally homologous to type I ribonucleotide reductase
Related PDB 1qhm
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 10648809
Journal FEBS Lett
Year 2000
Volume 466
Pages 45-8
Authors Plaga W, Vielhaber G, Wallach J, Knappe J
Title Modification of Cys-418 of pyruvate formate-lyase by methacrylic acid, based on its radical mechanism
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 11154425
Journal Oral Microbiol Immunol
Year 2000
Volume 15
Pages 325-8
Authors Iwami Y, Takahashi-Abbe S, Takahashi N, Abbe K, Yamada T
Title Rate-limiting steps of glucose and sorbitol metabolism in Streptococcus mutans cells exposed to air
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 11665486
Journal Adv Protein Chem
Year 2001
Volume 58
Pages 1-45
Authors Frey PA, Booker SJ
Title Radical mechanisms of S-adenosylmethionine-dependent enzymes
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 11444864
Journal Biochem Biophys Res Commun
Year 2001
Volume 285
Pages 456-62
Authors Wagner AF, Schultz S, Bomke J, Pils T, Lehmann WD, Knappe J
Title YfiD of Escherichia coli and Y06I of bacteriophage T4 as autonomous glycyl radical cofactors reconstituting the catalytic center of oxygen-fragmented pyruvate formate-lyase.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 11300793
Journal Biochemistry
Year 2001
Volume 40
Pages 4123-30
Authors Zhang W, Wong KK, Magliozzo RS, Kozarich JW
Title Inactivation of pyruvate formate-lyase by dioxygen
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 11278506
Journal J Biol Chem
Year 2001
Volume 276
Pages 12924-7
Authors Krieger CJ, Roseboom W, Albracht SP, Spormann AM
Title A stable organic free radical in anaerobic benzylsuccinate synthase of Azoarcus sp. strain T
Related PDB
Related UniProtKB
[28]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 12454503
Journal Acta Crystallogr D Biol Crystallogr
Year 2002
Volume 58
Pages 2209-12
Authors Lehtio L, Leppanen VM, Kozarich JW, Goldman A
Title Structure of Escherichia coli pyruvate formate-lyase with pyruvate.
Related PDB 1mzo
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 12236732
Journal J Am Chem Soc
Year 2002
Volume 124
Pages 11270-1
Authors Walsby CJ, Ortillo D, Broderick WE, Broderick JB, Hoffman BM
Title An 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.
Related PDB
Related UniProtKB
[30]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 12163496
Journal J Biol Chem
Year 2002
Volume 277
Pages 40036-42
Authors Becker A, Kabsch W
Title X-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 PDB 1h16 1h17 1h18
Related UniProtKB

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

Created Updated
2005-03-30 2009-02-26