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
30751
15346
32816
PubChem 444493
6302
18971002
284
6816
87642
1060
1cm5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:CO3 Unbound Unbound
1cm5B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:CO3 Unbound Unbound
1h16A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:COA Bound:PYR
1h17A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:COA Analogue:OXM
1h18A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:PYR
1h18B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:PYR
1mzoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:PYR
1mzoB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:PYR
1qhmA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1qhmB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2pflA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2pflB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3pflA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:OXM
3pflB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ; GLY 734 mutant C418A, C419A
1cm5B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ; GLY 734 mutant C418A, C419A
1h16A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 418;CYS 419 GLY 734
1h17A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 418;CYS 419 GLY 734
1h18A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 418;CYS 419 GLY 734
1h18B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 418;CYS 419 GLY 734
1mzoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 418;CYS 419 GLY 734
1mzoB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 418;CYS 419 GLY 734
1qhmA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 1418;CYS 1419 deletion 1616-1759
1qhmB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 2418;CYS 2419 deletion 2616-2759
2pflA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 418;CYS 419 GLY 734
2pflB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 418;CYS 419 GLY 734
3pflA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 418;CYS 419 GLY 734
3pflB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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