Escherichia coli K-12 substr. MG1655 Protein: predicted enamine/imine deaminase

Gene: tdcF Accession Numbers: G7626 (EcoCyc), b3113, ECK3102

Synonyms: yhaR

Regulation Summary Diagram: ?

Regulation summary diagram for tdcF

Subunit composition of predicted enamine/imine deaminase = [TdcF]3
         predicted enamine/imine deaminase = TdcF

Experimental work in Salmonella enterica serovar Typhimurium has identified an enamime/imine deaminase activity as the biochemical function of the conserved YjgF protein family [Lambrecht12]. Crystal structures of TdcF have been solved; the protein is homotrimeric in the crystal structure [Burman03, Burman07].

The tdc operon shows catabolite repression; expression is induced under anaerobic conditions in the presence of L-threonine [Hesslinger98].

Citations: [Hesslinger98a]

Gene Citations: [Hagewood94, Sawers01]

Locations: cytosol

Map Position: [3,257,743 <- 3,258,132] (70.21 centisomes, 253°)
Length: 390 bp / 129 aa

Molecular Weight of Polypeptide: 14.007 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010240 , DIP:DIP-48213N , EchoBASE:EB2611 , EcoGene:EG12757 , EcoliWiki:b3113 , ModBase:P0AGL2 , OU-Microarray:b3113 , PortEco:tdcF , PR:PRO_000024042 , Protein Model Portal:P0AGL2 , RefSeq:NP_417583 , RegulonDB:G7626 , SMR:P0AGL2 , String:511145.b3113 , Swiss-Model:P0AGL2 , UniProt:P0AGL2

Relationship Links: InterPro:IN-FAMILY:IPR006056 , InterPro:IN-FAMILY:IPR006175 , InterPro:IN-FAMILY:IPR013813 , InterPro:IN-FAMILY:IPR019897 , Panther:IN-FAMILY:PTHR11803 , PDB:Structure:2UYJ , PDB:Structure:2UYK , PDB:Structure:2UYN , PDB:Structure:2UYP , Pfam:IN-FAMILY:PF01042 , Prosite:IN-FAMILY:PS01094

In Paralogous Gene Group: 494 (4 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for tdcF

GO Terms:

Biological Process: GO:0006566 - threonine metabolic process Inferred from experiment [Burman07]
GO:0070689 - L-threonine catabolic process to propionate Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0042802 - identical protein binding Inferred from experiment [Burman07]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0019239 - deaminase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

Gene Class: ORFs

Essentiality data for tdcF 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 No 37 Aerobic 7   No [Baba06, Comment 2]

Created 12-Oct-2012 by Keseler I , SRI International
Last-Curated ? 12-Oct-2012 by Keseler I , SRI International

Sequence Features

Protein sequence of predicted enamine/imine deaminase with features indicated

Feature Class Location Citations Comment
N6-pyridoxal-phosphate-Lys-Modification 58
UniProt: N6-(pyridoxal phosphate)lysine; Non-Experimental Qualifier: by similarity.
Protein-Segment 105 -> 107
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 120
UniProt: Substrate.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
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

Burman03: Burman JD, Stevenson CE, Hauton KA, Sawers G, Lawson DM (2003). "Crystallization and preliminary X-ray analysis of the E. coli hypothetical protein TdcF." Acta Crystallogr D Biol Crystallogr 59(Pt 6);1076-8. PMID: 12777779

Burman07: Burman JD, Stevenson CE, Sawers RG, Lawson DM (2007). "The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family." BMC Struct Biol 7;30. PMID: 17506874

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

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."

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

Hesslinger98a: Hesslinger C, Sawers G (1998). "The tdcE gene in Escherichia coli strain W3110 is separated from the rest of the tdc operon by insertion of IS5 elements." DNA Seq 9(3);183-8. PMID: 10520749

Lambrecht12: Lambrecht JA, Flynn JM, Downs DM (2012). "Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions." J Biol Chem 287(5);3454-61. PMID: 22094463

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

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

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

Kim11d: 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

Wu92a: 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

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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