Escherichia coli K-12 substr. MG1655 Protein: α subunit complex

Gene: ttdA Accession Numbers: EG11168 (EcoCyc), b3061, ECK3051

Synonyms: ygjA

Regulation Summary Diagram

Regulation summary diagram for ttdA

Component of: L-tartrate dehydratase (summary available)

Subunit composition of α subunit complex = [TtdA]2
         L-tartrate dehydratase, α subunit = TtdA

The ttdA gene encodes the α-subunit of the L-tartrate dehydratase enzyme [Reaney93] and is expressed in exponentially growing cells [Nesin87].

Expression of ttdA is activated by the LysR-type transcriptional activator TtdR in the presence of L-tartrate and meso-tartrate and is repressed by O2 and nitrate (Unden, Paris). Binding of TtdR to the ttdA-ttdR intergenic region has been shown [Kim09b]. Anaerobic induction depends on FNR [Kim09b].

TtdA appears to be involved in biofilm formation. A mutant with a deletion of ttdA shows a significant decrease in biofilm formation [Herzberg06].

Expression of ttdA increases 11-fold upon deletion of tqsA, which increases biofilm formation [Herzberg06].

Gene Citations: [Oshima06a, Kim07a]

Locations: cytosol

Map Position: [3,204,485 -> 3,205,396] (69.07 centisomes, 249°)
Length: 912 bp / 303 aa

Molecular Weight of Polypeptide: 32.734 kD (from nucleotide sequence)

pI: 6.29

Unification Links: ASAP:ABE-0010050, CGSC:33459, EchoBASE:EB1156, EcoGene:EG11168, EcoliWiki:b3061, OU-Microarray:b3061, PortEco:ttdA, PR:PRO_000024137, Pride:P05847, Protein Model Portal:P05847, RefSeq:NP_417533, RegulonDB:EG11168, String:511145.b3061, UniProt:P05847

Relationship Links: InterPro:IN-FAMILY:IPR004646, Pfam:IN-FAMILY:PF05681

In Paralogous Gene Group: 484 (3 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for ttdA

GO Terms:
Biological Process:
Inferred from experimentGO:0042710 - biofilm formation [Herzberg06]
Inferred by computational analysisGO:0008152 - metabolic process [UniProtGOA11a, GOA01, GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Rajagopala14, Arifuzzaman06]
Inferred by computational analysisGO:0008730 - L(+)-tartrate dehydratase activity [GOA01]
Inferred by computational analysisGO:0016829 - lyase activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: metabolismenergy metabolism, carbonfermentation

Essentiality data for ttdA knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
Yes [Feist07, Comment 3]

Subunit of: L-tartrate dehydratase

Synonyms: L-Ttd

Subunit composition of L-tartrate dehydratase = [(TtdA)2][(TtdB)2]
         α subunit complex = (TtdA)2
                 L-tartrate dehydratase, α subunit = TtdA
         β subunit complex = (TtdB)2
                 L-tartrate dehydratase, β subunit = TtdB

E.coli is capable of degrading tartrate under aerobic or anaerobic conditions. L-tartrate dehydratase is induced during anaerobic growth on glycerol plus L- and meso-tartrates [Reaney93].

Molecular Weight: 105.0 kD (experimental) [Reaney93]

Enzymatic reaction of: L-tartrate dehydratase

Inferred from experiment

Synonyms: L+-tartrate dehydratase, (R,R)-tartrate hydro-lyase, tartrate dehydratase

EC Number:

L-tartrate ⇄ oxaloacetate + H2O

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

Alternative Substrates [ Comment 4]:

L-tartrate dehydratase is a stereospecific enzyme that is induced during anaerobic growth with glycerol. The enzyme has not been fully characterized. [Reaney93]

Cofactors or Prosthetic Groups: a [FeS] iron-sulfur cluster [Bairoch93]

Sequence Features

Protein sequence of L-tartrate dehydratase, alpha subunit with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 11
Inferred by curator[Nesin87, Reaney93, UniProt15]
UniProt: (in Ref. 1 and 2).
Pfam PF05681 16 -> 284
Inferred by computational analysis[Finn14]
Fumerase : Fumarate hydratase (Fumerase)
Metal-Binding-Site 71
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur.
Metal-Binding-Site 190
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur.
Sequence-Conflict 231 -> 232
Inferred by curator[Nesin87, Reaney93, UniProt15]
UniProt: (in Ref. 1 and 2).
Metal-Binding-Site 277
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur.

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


10/20/97 Gene b3061 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11168; confirmed by SwissProt match.


Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

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

Bairoch93: Bairoch A, Boeckmann B (1993). "The SWISS-PROT protein sequence data bank, recent developments." Nucleic Acids Res. 21:3093-3096. PMID: 8332529

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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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."

Herzberg06: Herzberg M, Kaye IK, Peti W, Wood TK (2006). "YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport." J Bacteriol 188(2);587-98. PMID: 16385049

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

Kim07a: Kim OB, Unden G (2007). "The L-tartrate/succinate antiporter TtdT (YgjE) of L-tartrate fermentation in Escherichia coli." J Bacteriol 189(5);1597-603. PMID: 17172328

Kim09b: Kim OB, Reimann J, Lukas H, Schumacher U, Grimpo J, Dunnwald P, Unden G (2009). "Regulation of tartrate metabolism by TtdR and relation to the DcuS-DcuR-regulated C4-dicarboxylate metabolism of Escherichia coli." Microbiology 155(Pt 11);3632-40. PMID: 19661178

Nesin87: Nesin M, Lupski JR, Svec P, Godson GN (1987). "Possible new genes as revealed by molecular analysis of a 5-kb Escherichia coli chromosomal region 5' to the rpsU-dnaG-rpoD macromolecular-synthesis operon." Gene 51(2-3);149-61. PMID: 3297921

Oshima06a: Oshima T, Biville F (2006). "Functional identification of ygiP as a positive regulator of the ttdA-ttdB-ygjE operon." Microbiology 152(Pt 7);2129-35. PMID: 16804186

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

Reaney93: Reaney SK, Begg C, Bungard SJ, Guest JR (1993). "Identification of the L-tartrate dehydratase genes (ttdA and ttdB) of Escherichia coli and evolutionary relationship with the class I fumarase genes." J Gen Microbiol 1993;139 ( Pt 7);1523-30. PMID: 8371115

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

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

Other References Related to Gene Regulation

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

Teramoto10: Teramoto J, Yoshimura SH, Takeyasu K, Ishihama A (2010). "A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions." Nucleic Acids Res 38(11);3605-18. PMID: 20156994

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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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