Escherichia coli K-12 substr. MG1655 Polypeptide: 2-ketobutyrate formate-lyase/pyruvate formate-lyase 4, inactive

Gene: tdcE Accession Numbers: G7627 (EcoCyc), b3114, ECK3103

Synonyms: yhaS

Regulation Summary Diagram: ?

Regulation summary diagram for tdcE

Alternative forms of 2-ketobutyrate formate-lyase/pyruvate formate-lyase 4, inactive: 2-ketobutyrate formate-lyase / pyruvate formate-lyase 4 (extended summary available)

Gene Citations: [Hagewood94, Sawers01]

Locations: cytosol, membrane

Map Position: [3,258,146 <- 3,260,440] (70.22 centisomes, 253°)
Length: 2295 bp / 764 aa

Molecular Weight of Polypeptide: 85.935 kD (from nucleotide sequence), 85.0 kD (experimental) [Hesslinger98 ]

Isozyme Sequence Similarity:

Unification Links: ASAP:ABE-0010242 , DIP:DIP-10972N , EchoBASE:EB2612 , EcoGene:EG12758 , EcoliWiki:b3114 , Mint:MINT-1231745 , ModBase:P42632 , OU-Microarray:b3114 , PortEco:tdcE , PR:PRO_000024041 , Protein Model Portal:P42632 , RefSeq:YP_026205 , RegulonDB:G7627 , SMR:P42632 , String:511145.b3114 , Swiss-Model:P42632 , UniProt:P42632

Relationship Links: InterPro:IN-FAMILY:IPR001150 , InterPro:IN-FAMILY:IPR004184 , InterPro:IN-FAMILY:IPR005949 , InterPro:IN-FAMILY:IPR019777 , Pfam:IN-FAMILY:PF01228 , Pfam:IN-FAMILY:PF02901 , Prosite:IN-FAMILY:PS00850 , Prosite:IN-FAMILY:PS51149 , Prosite:IN-FAMILY:PS51554

In Paralogous Gene Group: 205 (7 members)

In Reactions of unknown directionality:

Not in pathways:
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

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for tdcE

GO Terms:

Biological Process: GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
GO:0070689 - L-threonine catabolic process to propionate Inferred by curator Inferred by computational analysis [UniProtGOA12, Hesslinger98]
Molecular Function: GO:0043875 - 2-ketobutyrate formate-lyase activity Inferred from experiment [Hesslinger98]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0008861 - formate C-acetyltransferase activity Inferred by computational analysis [GOA01a, GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016746 - transferase activity, transferring acyl groups Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA01, Hesslinger98, Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization amino acids
metabolism central intermediary metabolism threonine catabolism
metabolism energy metabolism, carbon fermentation

Essentiality data for tdcE 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]

Sequence Features

Protein sequence of 2-ketobutyrate formate-lyase/pyruvate formate-lyase 4, inactive with features indicated

Feature Class Location Citations Comment
Conserved-Region 7 -> 629
UniProt: PFL.
Active-Site 423
UniProt: S-acetylcysteine intermediate; Non-Experimental Qualifier: by similarity;
Active-Site 424
UniProt: Cysteine radical intermediate; Non-Experimental Qualifier: by similarity;
Conserved-Region 636 -> 764
UniProt: Glycine radical;
Glycyl-Radical-Modification 739
UniProt: Glycine radical; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Hagewood94: Hagewood BT, Ganduri YL, Datta P (1994). "Functional analysis of the tdcABC promoter of Escherichia coli: roles of TdcA and TdcR." J Bacteriol 1994;176(20);6214-20. PMID: 7928991

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

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Sawers01: Sawers G (2001). "A novel mechanism controls anaerobic and catabolite regulation of the Escherichia coli tdc operon." Mol Microbiol 39(5);1285-98. PMID: 11251844

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

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

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

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

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Other References Related to Gene Regulation

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Kim11b: Kim M, Lim S, Ryu S (2011). "Comparison of tdcA Expression Between Escherichia coli and Salmonella enterica Serovar Typhimurium." J Microbiol Biotechnol 21(3);252-5. PMID: 21464594

Wu92: Wu Y, Patil RV, Datta P (1992). "Catabolite gene activator protein and integration host factor act in concert to regulate tdc operon expression in Escherichia coli." J Bacteriol 1992;174(21);6918-27. PMID: 1328166

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

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 19.0 on Tue Oct 6, 2015, BIOCYC14B.