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



Gene: ilvA Accession Numbers: EG10493 (EcoCyc), b3772, ECK3764

Synonyms: ile, threonine dehydratase

Regulation Summary Diagram: ?

Subunit composition of threonine deaminase = [IlvA]4

Summary:
Threonine deaminase (IlvA) carries out the first step in the synthesis of isoleucine. IlvA catalyzes the breakdown of L-threonine to generate 2-oxobutanoate and ammonia [Umbarger56, Umbarger57, Ramakrishnan64, Ramakrishnan65, Ramakrishnan65a]. Although the conversion of threonine into oxobutanoate is also the first step in the pathway of threonine degradation, IlvA is not thought to play a role in that pathway. This expectation is bolstered by the presence of an oxygen-responsive promoter for ilvA and the anaerobic nature of the degradation pathway.

Threonine deaminase is a tetramer [Grimminger73]. It has been alternately reported that either two or four pyridoxal phosphate molecules bind per tetramer [Koerner75, Eisenstein91]. In the complete absence of pyridoxal phosphate, the enzyme dissociates into nonfunctional 102 kD dimers [Calhoun73]. It has also been suggested that IlvA has several active multimeric forms, rather than being solely active as a tetramer [Kagan75]. The regulatory small molecules valine and isoleucine both bind threonine deaminase at four molecules per tetramer, the former cooperatively [Eisenstein94]. Isoleucine binds only twice per tetramer [Koerner75]. Crystal structures of threonine deaminase to 2.8 and 2.9 Å resolution reveal that it is a dimer of dimers, consisting of a set of carboxy-terminal regulatory domains projecting outward from a core of pyridoxal-containing amino-termini [Gallagher98a, Gallagher98b]. The regulatory domains possessed two effector-binding sites [Chen13].

Valine and isoleucine work to promote states with high and low affinity, respectively, for threonine. Isoleucine also appears to directly impact catalysis [Eisenstein95].

IlvA is cotranslated with IlvD [Harms88]. In addition to this contranslation, ilvA can also be transcribed and translated separately from its own oxygen-sensitive promoter [Lopes89].

IlvA abundance increases following treatment of cells with glycyl-leucine [Vonder72].

Mutations in ilvA code for enzymes with significantly reduced threonine deaminase activity, while overexpression of threonine demaminase resulted in growth inhibition most likely due to accumulation of toxic levels of α-ketobutyrate [Fisher93]. Inhibition of threonine demaminase is involved in homocysteine toxicity [Tuite05].

Gene Citations: [Sameshima89, Calhoun85, Parekh97, Driver85, Lawther87]

Locations: cytosol

Map Position: [3,953,354 -> 3,954,898] (85.21 centisomes)
Length: 1545 bp / 514 aa

Molecular Weight of Polypeptide: 56.195 kD (from nucleotide sequence)

pI: 6.04

Isozyme Sequence Similarity:
TdcB: YES

Unification Links: ASAP:ABE-0012321 , CGSC:609 , DIP:DIP-10018N , EchoBASE:EB0488 , EcoGene:EG10493 , EcoliWiki:b3772 , Mint:MINT-1305200 , ModBase:P04968 , OU-Microarray:b3772 , PortEco:ilvA , PR:PRO_000023001 , Pride:P04968 , Protein Model Portal:P04968 , RefSeq:NP_418220 , RegulonDB:EG10493 , SMR:P04968 , String:511145.b3772 , UniProt:P04968

Relationship Links: InterPro:IN-FAMILY:IPR000634 , InterPro:IN-FAMILY:IPR001721 , InterPro:IN-FAMILY:IPR001926 , InterPro:IN-FAMILY:IPR005787 , PDB:Structure:1TDJ , Pfam:IN-FAMILY:PF00291 , Pfam:IN-FAMILY:PF00585 , Prosite:IN-FAMILY:PS00165 , Prosite:IN-FAMILY:PS51672

In Paralogous Gene Group: 362 (8 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006566 - threonine metabolic process Inferred from experiment [Umbarger57]
GO:0009082 - branched-chain amino acid biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, Williams78]
GO:0009097 - isoleucine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA01, Fisher93, Favre74, Calhoun73]
GO:0006520 - cellular amino acid metabolic process Inferred by computational analysis [GOA01]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004794 - L-threonine ammonia-lyase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Fisher93, Favre74, Eisenstein91, Calhoun73]
GO:0016597 - amino acid binding Inferred from experiment [Eisenstein91]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment Inferred by computational analysis [GOA01, Eisenstein91]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids isoleucine/valine

Essentiality data for ilvA 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 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 3]
M9 medium with 1% glycerol No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 4]

Credits:
Curated 24-Sep-2007 by Shearer A , SRI International
Last-Curated ? 08-Oct-2013 by Kubo A , SRI International


Enzymatic reaction of: threonine deaminase

Synonyms: L-threonine hydro-lyase (deaminating), threonine dehydratase

L-threonine <=> (2Z)-2-aminobut-2-enoate + H2O + H+

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

The reaction is irreversible in the direction shown.

In Pathways: superpathway of threonine metabolism , superpathway of leucine, valine, and isoleucine biosynthesis , isoleucine biosynthesis I (from threonine)

Summary:
Inhibition by cysteine is partially competitive with respect to threonine [Harris81].

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Umbarger57, Umbarger56, Eisenstein91]

Activators (Unknown Mechanism): L-valine [Squires81]

Inhibitors (Other): L-cysteine [Harris81]

Inhibitors (Unknown Mechanism): D-cysteine [Soutourina01] , isoleucine tetrazole [Willshaw75] , L-isoleucine [Vonder72, Umbarger57, Umbarger56] , L-leucine [Vonder72]

Primary Physiological Regulators of Enzyme Activity: L-cysteine , L-isoleucine , L-leucine , L-valine

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-threonine
8000.0
[Eisenstein91]

pH(opt): 8-10 [Calhoun73]


Sequence Features

Feature Class Location Citations Comment
N6-pyridoxal-phosphate-Lys-Modification 62
[UniProt11a]
UniProt: N6-(pyridoxal phosphate)lysine.
Amino-Acid-Sites-That-Bind 89
[UniProt12a]
UniProt: Pyridoxal phosphate.
Sequence-Conflict 120
[Garrison86, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 2);
Sequence-Conflict 140
[Garrison86, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 2; AAA24014/AAA67575);
Protein-Segment 189 -> 192
[UniProt12a]
UniProt: Pyridoxal phosphate binding; Sequence Annotation Type: region of interest.
Sequence-Conflict 195
[Garrison86, UniProt10]
Alternate sequence: G → C; UniProt: (in Ref. 2; AAA24014);
Sequence-Conflict 243
[Lawther87, UniProt10]
Alternate sequence: A → G; UniProt: (in Ref. 3; AAA24024);
Amino-Acid-Sites-That-Bind 315
[UniProt12a]
UniProt: Pyridoxal phosphate.
Sequence-Conflict 334
[Garrison86, UniProt10]
Alternate sequence: G → V; UniProt: (in Ref. 2; AAA24014);
Conserved-Region 339 -> 411
[UniProt13]
UniProt: ACT-like 1.
Conserved-Region 434 -> 504
[UniProt13]
UniProt: ACT-like 2.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3772 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10493; confirmed by SwissProt match.


References

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

Calhoun73: Calhoun DH, Rimerman RA, Hatfield GW (1973). "Threonine deaminase from Escherichia coli. I. Purification and properties." J Biol Chem 1973;248(10);3511-6. PMID: 4573981

Calhoun85: Calhoun DH, Wallen JW, Traub L, Gray JE, Kung HF (1985). "Internal promoter in the ilvGEDA transcription unit of Escherichia coli K-12." J Bacteriol 161(1);128-32. PMID: 3917997

Chen13: Chen L, Chen Z, Zheng P, Sun J, Zeng AP (2013). "Study and reengineering of the binding sites and allosteric regulation of biosynthetic threonine deaminase by isoleucine and valine in Escherichia coli." Appl Microbiol Biotechnol 97(7);2939-49. PMID: 22669632

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

Driver85: Driver RP, Lawther RP (1985). "Physical analysis of deletion mutations in the ilvGEDA operon of Escherichia coli K-12." J Bacteriol 162(2);598-606. PMID: 2985538

Eisenstein91: Eisenstein E (1991). "Cloning, expression, purification, and characterization of biosynthetic threonine deaminase from Escherichia coli." J Biol Chem 1991;266(9);5801-7. PMID: 2005118

Eisenstein94: Eisenstein E, Yu HD, Schwarz FP (1994). "Cooperative binding of the feedback modifiers isoleucine and valine to biosynthetic threonine deaminase from Escherichia coli." J Biol Chem 269(47);29423-9. PMID: 7961922

Eisenstein95: Eisenstein E (1995). "Allosteric regulation of biosynthetic threonine deaminase from Escherichia coli: effects of isoleucine and valine on active-site ligand binding and catalysis." Arch Biochem Biophys 316(1);311-8. PMID: 7840631

Favre74: Favre R, Iaccarino M, Levinthal M (1974). "Complementation between different mutations in the ilvA gene of Escherichia coli K-12." J Bacteriol 119(3);1069-71. PMID: 4604254

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

Fisher93: Fisher KE, Eisenstein E (1993). "An efficient approach to identify ilvA mutations reveals an amino-terminal catalytic domain in biosynthetic threonine deaminase from Escherichia coli." J Bacteriol 175(20);6605-13. PMID: 8407838

Gallagher98a: Gallagher DT, Gilliland GL, Xiao G, Zondlo J, Fisher KE, Chinchilla D, Eisenstein E (1998). "Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase." Structure 6(4);465-75. PMID: 9562556

Gallagher98b: Gallagher DT, Eisenstein E, Fisher KE, Zondlo J, Chinchilla D, Yu HD, Dill J, Winborne E, Ducote K, Xiao G, Gilliland GL (1998). "Polymorphous crystallization and diffraction of threonine deaminase from Escherichia coli." Acta Crystallogr D Biol Crystallogr 54(Pt 3);467-9. PMID: 9761930

Garrison86: Garrison E., Harms E., Umbarger H.E. (1986). Data submission to EMBL/GenBank/DDBJ databases on 1986-08.

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.

Grimminger73: Grimminger H, Rahimi-Laridjani I, Koerner K, Lingens F (1973). "Purification of threonine deaminase from Escherichia coli." FEBS Lett 35(2);273-5. PMID: 4582943

Harms88: Harms E, Higgins E, Chen JW, Umbarger HE (1988). "Translational coupling between the ilvD and ilvA genes of Escherichia coli." J Bacteriol 170(10);4798-807. PMID: 3049548

Harris81: Harris CL (1981). "Cysteine and growth inhibition of Escherichia coli: threonine deaminase as the target enzyme." J Bacteriol 145(2);1031-5. PMID: 7007336

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

Kagan75: Kagan ZS, Dorozhko AI, Kovaleva SV, Yakovleva LI (1975). "Studies of homogeneous "biosynthetic" L-threonine dehydratase from Escherichia coli K-12. Some kinetic properties and molecular multiplicity." Biochim Biophys Acta 403(1);208-20. PMID: 240428

Koerner75: Koerner K, Rahimi-Laridjani I, Grimminger H (1975). "Purification of biosynthetic threonine deaminase from Escherichia coli." Biochim Biophys Acta 397(1);220-30. PMID: 1096954

Lawther87: Lawther RP, Wek RC, Lopes JM, Pereira R, Taillon BE, Hatfield GW (1987). "The complete nucleotide sequence of the ilvGMEDA operon of Escherichia coli K-12." Nucleic Acids Res 1987;15(5);2137-55. PMID: 3550695

Lopes89: Lopes JM, Lawther RP (1989). "Physical identification of an internal promoter, ilvAp, in the distal portion of the ilvGMEDA operon." Gene 76(2);255-69. PMID: 2473940

Parekh97: Parekh BS, Hatfield GW (1997). "Growth rate-related regulation of the ilvGMEDA operon of Escherichia coli K-12 is a consequence of the polar frameshift mutation in the ilvG gene of this strain." J Bacteriol 1997;179(6);2086-8. PMID: 9068661

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

Ramakrishnan64: Ramakrishnan T, Adelberg EA (1964). "Regulatory mechanisms in the biosynthesis of isoleucine and valine. I. Genetic derepression of enzyme formation." J Bacteriol 87;566-73. PMID: 14127571

Ramakrishnan65: Ramakrishnan T, Adelberg EA (1965). "Regulatory mechanisms in the biosynthesis of isoleucine and valine. II. Identification of two operator genes." J Bacteriol 89;654-60. PMID: 14273640

Ramakrishnan65a: Ramakrishnan T, Adelberg EA (1965). "Regulatory mechanisms in the biosynthesis of isoleucine and valine. 3. Map order of the structural genes and operator genes." J Bacteriol 89;661-4. PMID: 14273641

Sameshima89: Sameshima JH, Wek RC, Hatfield GW (1989). "Overlapping transcription and termination of the convergent ilvA and ilvY genes of Escherichia coli." J Biol Chem 1989;264(2);1224-31. PMID: 2642900

Soutourina01: Soutourina J, Blanquet S, Plateau P (2001). "Role of D-cysteine desulfhydrase in the adaptation of Escherichia coli to D-cysteine." J Biol Chem 276(44);40864-72. PMID: 11527960

Squires81: Squires CH, Levinthal M, De Felice M (1981). "A role for threonine deaminase in the regulation of alpha-acetolactate biosynthesis in Escherichia coli K12." J Gen Microbiol 1981;127, pt 1;19-25. PMID: 7040602

Tuite05: Tuite NL, Fraser KR, O'byrne CP (2005). "Homocysteine toxicity in Escherichia coli is caused by a perturbation of branched-chain amino acid biosynthesis." J Bacteriol 187(13);4362-71. PMID: 15968045

Umbarger56: Umbarger HE, Brown B (1956). "Threonine deamination in Escherichia coli. I. D- and L-threonine deaminase activities of cell-free extracts." J Bacteriol 71(4);443-9. PMID: 13319259

Umbarger57: Umbarger HE, Brown B (1957). "Threonine deamination in Escherichia coli. II. Evidence for two L-threonine deaminases." J Bacteriol 73(1);105-12. PMID: 13405870

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

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

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 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."

Vonder72: Vonder Haar RA, Umbarger HE (1972). "Isoleucine and valine metabolism in Escherichia coli. XIX. Inhibition of isoleucine biosynthesis by glycyl-leucine." J Bacteriol 112(1);142-7. PMID: 4562390

Williams78: Williams AL, Whitfield SM, Williams LS (1978). "Synthesis and activities of branched-chain aminoacyl-tRNA synthetases in threonine deaminase mutants of Escherichia coli." J Bacteriol 134(1);92-9. PMID: 348689

Willshaw75: Willshaw GA, Tristram H (1975). "Inhibition of Escherichia coli isoleucine biosynthesis by isoleucine tetrazole." J Bacteriol 123(3);862-70. PMID: 1099080

Other References Related to Gene Regulation

Adams85: Adams CW, Rosenberg M, Hatfield GW (1985). "Analysis of in vivo RNA transcription products of the ilvGEDA attenuator region of Escherichia coli K12." J Biol Chem 1985;260(14);8538-44. PMID: 2409090

Lisser93: Lisser S, Margalit H (1993). "Compilation of E. coli mRNA promoter sequences." Nucleic Acids Res 21(7);1507-16. PMID: 8479900

Pagel91: Pagel JM, Hatfield GW (1991). "Integration host factor-mediated expression of the ilvGMEDA operon of Escherichia coli." J Biol Chem 1991;266(3);1985-96. PMID: 1703160

Pagel92: Pagel JM, Winkelman JW, Adams CW, Hatfield GW (1992). "DNA topology-mediated regulation of transcription initiation from the tandem promoters of the ilvGMEDA operon of Escherichia coli." J Mol Biol 1992;224(4);919-35. PMID: 1569580

Parekh96: Parekh BS, Hatfield GW (1996). "Transcriptional activation by protein-induced DNA bending: evidence for a DNA structural transmission model." Proc Natl Acad Sci U S A 1996;93(3);1173-7. PMID: 8577735

Parekh96a: Parekh BS, Sheridan SD, Hatfield GW (1996). "Effects of integration host factor and DNA supercoiling on transcription from the ilvPG promoter of Escherichia coli." J Biol Chem 1996;271(34);20258-64. PMID: 8702758

Rhee96: Rhee KY, Parekh BS, Hatfield GW (1996). "Leucine-responsive regulatory protein-DNA interactions in the leader region of the ilvGMEDA operon of Escherichia coli." J Biol Chem 1996;271(43);26499-507. PMID: 8900118

Subrahmanyam80: Subrahmanyam CS, Noti JD, Umbarger HE (1980). "Regulation of ilvEDA expression occurs upstream of ilvG in Escherichia coli: additional evidence for an ilvGEDA operon." J Bacteriol 144(1);279-90. PMID: 6252193

Tsui88: Tsui P, Freundlich M (1988). "Integration host factor binds specifically to sites in the ilvGMEDA operon in Escherichia coli." J Mol Biol 203(3);817-20. PMID: 3145340

Wek86a: Wek RC, Hatfield GW (1986). "Examination of the internal promoter, PE, in the ilvGMEDA operon of E. coli K-12." Nucleic Acids Res 1986;14(6);2763-77. PMID: 2421252


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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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