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Escherichia coli K-12 substr. MG1655 Enzyme: pyruvate formate-lyase activating enzyme



Gene: pflA Accession Numbers: EG10028 (EcoCyc), b0902, ECK0893

Synonyms: act

Regulation Summary Diagram: ?

Citations: [Yang09a]

Locations: cytosol

Map Position: [949,563 <- 950,303] (20.47 centisomes)
Length: 741 bp / 246 aa

Molecular Weight of Polypeptide: 28.204 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003068 , CGSC:35839 , DIP:DIP-35915N , EchoBASE:EB0027 , EcoGene:EG10028 , EcoliWiki:b0902 , OU-Microarray:b0902 , PortEco:pflA , PR:PRO_000023516 , Pride:P0A9N4 , Protein Model Portal:P0A9N4 , RefSeq:NP_415422 , RegulonDB:EG10028 , SMR:P0A9N4 , String:511145.b0902 , UniProt:P0A9N4

Relationship Links: InterPro:IN-FAMILY:IPR001989 , InterPro:IN-FAMILY:IPR006638 , InterPro:IN-FAMILY:IPR007197 , InterPro:IN-FAMILY:IPR012838 , PDB:Structure:3C8F , PDB:Structure:3CB8 , Pfam:IN-FAMILY:PF04055 , Prosite:IN-FAMILY:PS01087 , Smart:IN-FAMILY:SM00729

In Paralogous Gene Group: 205 (7 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006006 - glucose metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0016491 - oxidoreductase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Yang09a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0043365 - [formate-C-acetyltransferase]-activating enzyme activity Inferred by computational analysis [GOA01, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: information transfer protein related posttranslational modification
metabolism energy metabolism, carbon anaerobic respiration
regulation type of regulation posttranscriptional inhibition / activation of enzymes

Essentiality data for pflA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Enzymatic reaction of: pyruvate formate-lyase activating enzyme

Synonyms: activase, PFL-activating enzyme

EC Number: 1.97.1.4

2-ketobutyrate formate-lyase/pyruvate formate-lyase 4, inactive + a reduced flavodoxin + S-adenosyl-L-methionine <=> 5'-deoxyadenosine + 2-ketobutyrate formate-lyase / pyruvate formate-lyase 4 + an oxidized flavodoxin

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is irreversible in the direction shown.

EC Number: 1.97.1.4

pyruvate formate-lyase (inactive) + a reduced flavodoxin + S-adenosyl-L-methionine <=> 5'-deoxyadenosine + L-methionine + pyruvate formate-lyase / 2-ketobutyrate formate-lyase + an oxidized flavodoxin

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is irreversible in the direction shown.

Summary:
Pyruvate formate-lyase activating enzyme, or activase, functions as an activator of pyruvate formate-lyase under anaerobic conditions by generating an organic free radical using S-adenosylmethionine and reduced flavodoxin as co-substrates to produce 5'-deoxyadenosine. The activase is also capable of of activating the tdcE encoded 2-ketobutyrate/pyruvate formate-lyase. [Rodel88, Hesslinger98]

Citations: [Conradt84]

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Kulzer98, Broderick97]

Activators (Allosteric): pyruvate [Knappe90]

Activators (Unknown Mechanism): free Fe++ [Knappe90]

Inhibitors (Competitive): S-adenosyl-L-homocysteine [Knappe90, Comment 5]

Kinetic Parameters:

Substrate
Km (μM)
Citations
S-adenosyl-L-methionine
2.8
[Wong93, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[UniProt10]
UniProt: Removed;
Chain 2 -> 246
[UniProt09]
UniProt: Pyruvate formate-lyase 1-activating enzyme;
Metal-Binding-Site 30
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 34
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 37
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S-S-AdoMet); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0902 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10028; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Broderick97: Broderick JB, Duderstadt RE, Fernandez DC, Wojtuszewski K, Henshaw TF, Johnson MK "Pyruvate Formate-Lyase Activating Enzyme Is an Iron-Sulfur Protein." Journal of the American Chemical Society 119:7396-7397 (1997).

Conradt84: Conradt H, Hohmann-Berger M, Hohmann HP, Blaschkowski HP, Knappe J (1984). "Pyruvate formate-lyase (inactive form) and pyruvate formate-lyase activating enzyme of Escherichia coli: isolation and structural properties." Arch Biochem Biophys 1984;228(1);133-42. PMID: 6364987

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hesslinger98: Hesslinger C, Fairhurst SA, Sawers G (1998). "Novel keto acid formate-lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L-threonine to propionate." Mol Microbiol 1998;27(2);477-92. PMID: 9484901

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Knappe90: Knappe J, Sawers G (1990). "A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system of Escherichia coli." FEMS Microbiol Rev 1990;6(4);383-98. PMID: 2248795

Kulzer98: Kulzer R, Pils T, Kappl R, Huttermann J, Knappe J (1998). "Reconstitution and characterization of the polynuclear iron-sulfur cluster in pyruvate formate-lyase-activating enzyme. Molecular properties of the holoenzyme form." J Biol Chem 1998;273(9);4897-903. PMID: 9478932

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Rodel88: Rodel W, Plaga W, Frank R, Knappe J (1988). "Primary structures of Escherichia coli pyruvate formate-lyase and pyruvate-formate-lyase-activating enzyme deduced from the DNA nucleotide sequences." Eur J Biochem 177(1);153-8. PMID: 3053170

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wong93: Wong KK, Murray BW, Lewisch SA, Baxter MK, Ridky TW, Ulissi-DeMario L, Kozarich JW (1993). "Molecular properties of pyruvate formate-lyase activating enzyme." Biochemistry 1993;32(51);14102-10. PMID: 8260492

Yang09a: Yang J, Naik SG, Ortillo DO, Garcia-Serres R, Li M, Broderick WE, Huynh BH, Broderick JB (2009). "The iron-sulfur cluster of pyruvate formate-lyase activating enzyme in whole cells: cluster interconversion and a valence-localized [4Fe-4S]2+ state." Biochemistry 48(39);9234-41. PMID: 19711960

Other References Related to Gene Regulation

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Thu Nov 20, 2014, BIOCYC14B.