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Escherichia coli K-12 substr. MG1655 Enzyme: 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

Summary:
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: 105000 kD (experimental) [Reaney93 ]

Gene-Reaction Schematic: ?


Enzymatic reaction of: L-tartrate dehydratase

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

EC Number: 4.2.1.32

L-tartrate <=> oxaloacetate + H2O

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

This reaction is reversible.

Alternative Substrates [Comment 1]:

Summary:
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: [FeS] iron-sulfur cluster [Bairoch93]


Subunit of L-tartrate dehydratase: α subunit complex

Synonyms: ygjA

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

Locations: cytosol

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

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

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

pI: 6.29

GO Terms:

Biological Process: GO:0042710 - biofilm formation Inferred from experiment [Herzberg06]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11, GOA01a, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman06]
GO:0008730 - L(+)-tartrate dehydratase activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism energy metabolism, carbon fermentation

Unification Links: EcoliWiki:b3061 , PR:PRO_000024137 , Pride:P05847 , Protein Model Portal:P05847 , RefSeq:NP_417533 , String:511145.b3061 , UniProt:P05847

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

Summary:
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 [Kim09a]. Anaerobic induction depends on FNR [Kim09a].

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, Kim07c]

Essentiality data for ttdA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
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]

Subunit of L-tartrate dehydratase: β subunit complex

Synonyms: ygjB

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

Locations: cytosol

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

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

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

pI: 6.81

GO Terms:

Biological Process: GO:0009408 - response to heat Inferred from experiment [Krisko14]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11, GOA01a, GOA01]
Molecular Function: GO:0008730 - L(+)-tartrate dehydratase activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0016836 - hydro-lyase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism energy metabolism, carbon fermentation

Unification Links: EcoliWiki:b3062 , PR:PRO_000024138 , Protein Model Portal:P0AC35 , RefSeq:NP_417534 , SMR:P0AC35 , String:511145.b3062 , UniProt:P0AC35

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

Summary:
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 [Krisko14].

Gene Citations: [Oshima06a, Kim07c]

Essentiality data for ttdB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 5]
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]

References

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

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.

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

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

Kim09a: 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

Krisko14: 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

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

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


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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 Dec 18, 2014, biocyc12.