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Escherichia coli K-12 substr. MG1655 Enzyme: threonine dehydrogenase



Gene: tdh Accession Numbers: EG10993 (EcoCyc), b3616, ECK3606

Regulation Summary Diagram: ?

Subunit composition of threonine dehydrogenase = [Tdh]4

Summary:
Threonine dehydrogenase (Tdh) catalyzes the conversion of L-threonine to the unstable intermediate L-2-amino-3-oxobutanoate, which can spontaneously decarboxylate yielding aminoacetone and CO2 or be converted to acetyl-CoA and glycine by the second enzyme in the catabolic pathway. This is the major catabolic pathway for threonine utilization. This two step pathway also provides an alternative route for glycine and serine biosynthesis in E. coli. [Craig90, Epperly91, Aronson89, Boylan81]

Tdh is a member of the zinc-containing long-chain alcohol/polyol dehydrogenase family [Aronson89, Epperly91]. The enzyme is damaged by micromolar concentrations of hydrogen peroxide in vitro due to oxidation of the cysteine residue [Anjem12].

Inactivation studies of Tdh have provided evidence for a catalytically essential arginine residue [Epperly89] as well as active site cysteine [Epperly91] and histidine [Marcus95] residues. Mutant studies have also identified functionally important residues [Chen95] including His-90 [Johnson98], and a possible catalytic zinc binding site at Cys-38 [Johnson98a].

Review: Reitzer, L. (2005) "Catabolism of Amino Acids and Related Compounds" EcoSal 3.4.7 [ECOSAL]

Gene Citations: [Ravnikar86, Landgraf94]

Locations: cytosol

Map Position: [3,788,343 <- 3,789,368] (81.65 centisomes)
Length: 1026 bp / 341 aa

Molecular Weight of Polypeptide: 37.239 kD (from nucleotide sequence), 35.0 kD (experimental) [Boylan81 ]

Molecular Weight of Multimer: 140.0 kD (experimental) [Boylan81]

pI: 6.32

Unification Links: ASAP:ABE-0011830 , CGSC:17584 , DIP:DIP-6855N , EchoBASE:EB0986 , EcoGene:EG10993 , EcoliWiki:b3616 , ModBase:P07913 , OU-Microarray:b3616 , PortEco:tdh , PR:PRO_000024044 , Pride:P07913 , Protein Model Portal:P07913 , RefSeq:NP_418073 , RegulonDB:EG10993 , SMR:P07913 , String:511145.b3616 , UniProt:P07913

Relationship Links: InterPro:IN-FAMILY:IPR002085 , InterPro:IN-FAMILY:IPR002328 , InterPro:IN-FAMILY:IPR004627 , InterPro:IN-FAMILY:IPR011032 , InterPro:IN-FAMILY:IPR013149 , InterPro:IN-FAMILY:IPR013154 , InterPro:IN-FAMILY:IPR016040 , Panther:IN-FAMILY:PTHR11695 , Pfam:IN-FAMILY:PF00107 , Pfam:IN-FAMILY:PF08240 , Prosite:IN-FAMILY:PS00059

In Paralogous Gene Group: 103 (13 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006564 - L-serine biosynthetic process Inferred from experiment [Ravnikar87]
GO:0006567 - threonine catabolic process Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Chen95]
GO:0019518 - L-threonine catabolic process to glycine Inferred by computational analysis [UniProtGOA12]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008198 - ferrous iron binding Inferred from experiment [Anjem12]
GO:0008270 - zinc ion binding Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Epperly91]
GO:0008743 - L-threonine 3-dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Anjem12, Boylan81]
GO:0016491 - oxidoreductase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Boylan81]
GO:0030145 - manganese ion binding Inferred from experiment [Boylan81, Craig86]
GO:0042802 - identical protein binding Inferred from experiment [Boylan81]
GO:0046870 - cadmium ion binding Inferred from experiment [Craig88]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, Boylan81]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Lasserre06]

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

Essentiality data for tdh 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]

Credits:
Last-Curated ? 15-Nov-2011 by Fulcher C , SRI International


Enzymatic reaction of: threonine dehydrogenase

Synonyms: threonine 3-dehydrogenase, L-threonine 3-dehydrogenase, L-threonine:NAD+ oxidoreductase

EC Number: 1.1.1.103

L-threonine + NAD+ <=> 2-amino-3-oxobutanoate + NADH + 2 H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for L-threonine: L-threonine amide , D-allothreonine

In Pathways: superpathway of threonine metabolism , threonine degradation III (to methylglyoxal) , threonine degradation II

Summary:
The enzyme was specific for NAD+ although it could also utilize several analogs of NAD+. NADP+ was inactive as a cofactor [Boylan81].

Cofactors or Prosthetic Groups: Fe2+ [Anjem12], Zn2+ [Comment 5]

Activators (Unknown Mechanism): Cd2+ [Craig88] , Mn2+ [Comment 6]

Inhibitors (Unknown Mechanism): cyclohexane-1,2-dione [Epperly89] , Cu2+ [Boylan81, Craig86] , Ni2+ [Boylan81, Craig86] , Be2+ [Craig86] , Hg2+ [Craig86] , Ag2+ [Craig86] , p-mercuribenzoate [Boylan81] , 5,5'-dithio-bis-2-nitrobenzoate [Boylan81] , 2-mercaptoethanol [Comment 7] , diacetyl [Epperly89] , phenylglyoxal [Epperly89] , 2,3-pentane-dione [Epperly89]

Primary Physiological Regulators of Enzyme Activity: diacetyl

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-threonine
6500.0
88.0
[Anjem12]
NAD+
270.0
[Anjem12]

pH(opt): 10.3 [Boylan81]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 38
[UniProt10a]
UniProt: Zinc 1; catalytic;
Metal-Binding-Site 63
[UniProt10]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 93
[UniProt10]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 96
[UniProt10]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 99
[UniProt10]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 107
[UniProt10]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 148
[UniProt10]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3616 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10993; confirmed by SwissProt match.


References

Anjem12: Anjem A, Imlay JA (2012). "Mononuclear iron enzymes are primary targets of hydrogen peroxide stress." J Biol Chem 287(19);15544-56. PMID: 22411989

Aronson89: Aronson BD, Somerville RL, Epperly BR, Dekker EE (1989). "The primary structure of Escherichia coli L-threonine dehydrogenase." J Biol Chem 1989;264(9);5226-32. PMID: 2647748

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

Boylan81: Boylan SA, Dekker EE (1981). "L-threonine dehydrogenase. Purification and properties of the homogeneous enzyme from Escherichia coli K-12." J Biol Chem 1981;256(4);1809-15. PMID: 6780553

Chen95: Chen YW, Dekker EE, Somerville RL (1995). "Functional analysis of E. coli threonine dehydrogenase by means of mutant isolation and characterization." Biochim Biophys Acta 1253(2);208-14. PMID: 8519804

Craig86: Craig PA, Dekker EE (1986). "L-threonine dehydrogenase from Escherichia coli K-12: thiol-dependent activation by Mn2+." Biochemistry 1986;25(8);1870-6. PMID: 3518793

Craig88: Craig PA, Dekker EE (1988). "Cd2+ activation of L-threonine dehydrogenase from Escherichia coli K-12." Biochim Biophys Acta 1988;957(2);222-9. PMID: 3056527

Craig90: Craig PA, Dekker EE (1990). "The sulfhydryl content of L-threonine dehydrogenase from Escherichia coli K-12: relation to catalytic activity and Mn2+ activation." Biochim Biophys Acta 1990;1037(1);30-8. PMID: 2104757

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

ECOSAL: "Escherichia coli and Salmonella: Cellular and Molecular Biology." Online edition.

Epperly89: Epperly BR, Dekker EE (1989). "Inactivation of Escherichia coli L-threonine dehydrogenase by 2,3-butanedione. Evidence for a catalytically essential arginine residue." J Biol Chem 1989;264(31);18296-301. PMID: 2681195

Epperly91: Epperly BR, Dekker EE (1991). "L-threonine dehydrogenase from Escherichia coli. Identification of an active site cysteine residue and metal ion studies." J Biol Chem 1991;266(10);6086-92. PMID: 2007567

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, 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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Johnson98: Johnson AR, Dekker EE (1998). "Site-directed mutagenesis of histidine-90 in Escherichia coli L-threonine dehydrogenase alters its substrate specificity." Arch Biochem Biophys 351(1);8-16. PMID: 9500838

Johnson98a: Johnson AR, Chen YW, Dekker EE (1998). "Investigation of a catalytic zinc binding site in Escherichia coli L-threonine dehydrogenase by site-directed mutagenesis of cysteine-38." Arch Biochem Biophys 358(2);211-21. PMID: 9784233

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

Landgraf94: Landgraf JR, Levinthal M, Danchin A (1994). "The role of H-NS in one carbon metabolism." Biochimie 1994;76(10-11);1063-70. PMID: 7748928

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

Marcus95: Marcus JP, Dekker EE (1995). "Identification of a second active site residue in Escherichia coli L-threonine dehydrogenase: methylation of histidine-90 with methyl p-nitrobenzenesulfonate." Arch Biochem Biophys 316(1);413-20. PMID: 7840645

Ravnikar86: Ravnikar PD, Somerville RL (1986). "Localization of the structural gene for threonine dehydrogenase in Escherichia coli." J Bacteriol 168(1);434-6. PMID: 3531182

Ravnikar87: Ravnikar PD, Somerville RL (1987). "Genetic characterization of a highly efficient alternate pathway of serine biosynthesis in Escherichia coli." J Bacteriol 169(6);2611-7. PMID: 3108237

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

UniProtGOA11a: 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

Aronson88: Aronson BD, Ravnikar PD, Somerville RL (1988). "Nucleotide sequence of the 2-amino-3-ketobutyrate coenzyme A ligase (kbl) gene of E. coli." Nucleic Acids Res 16(8);3586. PMID: 3287333

Fraenkel95: Fraenkel YM, Mandel Y, Friedberg D, Margalit H (1995). "Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon." Comput Appl Biosci 1995;11(4);379-87. PMID: 8521047

Rex91: Rex JH, Aronson BD, Somerville RL (1991). "The tdh and serA operons of Escherichia coli: mutational analysis of the regulatory elements of leucine-responsive genes." J Bacteriol 1991;173(19);5944-53. PMID: 1917830


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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 Sat Nov 22, 2014, biocyc14.