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

Gene: ttdB Accession Numbers: EG11169 (EcoCyc), b3062, ECK3052

Synonyms: ygjB

Regulation Summary Diagram

Regulation summary diagram for ttdB

Component of: L-tartrate dehydratase (summary available)

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

The ttdB gene encodes the beta subunit of L-tartrate dehydratase [Reaney93] and is expressed in exponentially growing cells [Nesin87]. Expression may be translationally coupled to TtdA [Reaney93].

ttdB shows differential codon adaptation, resulting in differential translation efficiency signatures, in thermophilic microbes. It was therefore predicted to play a role in the heat shock response. A ttdB deletion mutant was shown to be more sensitive than wild-type specifically to heat shock, but not other stresses [Kri14].

Gene Citations: [Oshima06a, Kim07c]

Locations: cytosol

Map Position: [3,205,393 -> 3,205,998] (69.09 centisomes, 249°)
Length: 606 bp / 201 aa

Molecular Weight of Polypeptide: 22.679 kD (from nucleotide sequence)

pI: 6.81

Unification Links: ASAP:ABE-0010052, CGSC:33462, EchoBASE:EB1157, EcoGene:EG11169, EcoliWiki:b3062, OU-Microarray:b3062, PortEco:ttdB, PR:PRO_000024138, Protein Model Portal:P0AC35, RefSeq:NP_417534, RegulonDB:EG11169, SMR:P0AC35, String:511145.b3062, UniProt:P0AC35

Relationship Links: InterPro:IN-FAMILY:IPR004647, Pfam:IN-FAMILY:PF05683

In Paralogous Gene Group: 318 (3 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for ttdB

GO Terms:
Biological Process:
Inferred from experimentGO:0009408 - response to heat [Kri14]
Inferred by computational analysisGO:0008152 - metabolic process [UniProtGOA11a, GOA01, GOA01a]
Molecular Function:
Inferred by computational analysisGO:0008730 - L(+)-tartrate dehydratase activity [GOA01]
Inferred by computational analysisGO:0016829 - lyase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016836 - hydro-lyase activity [GOA01a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: metabolismenergy metabolism, carbonfermentation

Essentiality data for ttdB knockouts:

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

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 5]:

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, beta subunit with features indicated

Feature Class Location Citations Comment
Pfam PF05683 9 -> 175
Inferred by computational analysis[Finn14]
Fumerase_C : Fumarase C-terminus
Active-Site 37
Inferred by computational analysis[UniProt15]
Sequence-Conflict 80 -> 85
Inferred by curator[Nesin87, Reaney93, UniProt15]
UniProt: (in Ref. 1 and 2).
Sequence-Conflict 165
Inferred by curator[Nesin87, Reaney93, UniProt15]
UniProt: (in Ref. 1 and 2).

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 b3062 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11169; confirmed by SwissProt match.


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

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."

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

Kim07c: 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

Kri14: Krisko A, Copi T, Gabaldon T, Lehner B, Supek F (2014). "Inferring gene function from evolutionary change in signatures of translation efficiency." Genome Biol 15(3);R44. PMID: 24580753

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

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

Kim09f: 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

Teramoto10a: 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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