Escherichia coli K-12 substr. MG1655 Enzyme: homoserine kinase

Gene: thrB Accession Numbers: EG10999 (EcoCyc), b0003, ECK0003

Regulation Summary Diagram: ?

Regulation summary diagram for thrB

Subunit composition of homoserine kinase = [ThrB]2

Homoserine kinase (ThrB) catalyzes the phosphorylation of homoserine to O-phospho-L-homoserine en route to generating threonine [Burr76, Shames84].

Though it is a substrate, homoserine can actually cause partial inhibition of the reaction at higher concentrations, with a Ki of ~2 mM [Shames84]. Substrate inhibition by high levels of ATP has also been observed [Chassagnole01]. ThrB has been subject to kinetic and mechanistic analysis [Shames84, Huo96]. The enzyme appears to have a second, regulatory binding site for L-homoserine [Shames84, Chassagnole01]. Site-directed mutagenesis has confirmed the role of Arg234 and the His residues H139 and H205 in substrate binding [Huo96a].

ThrB is required for growth of pdxB mutants on glucose and 3-hydroxyhomoserine or D-glycolaldehyde [Zhao96a]. Later, thrB was identified as a multicopy suppressor of the PLP auxotrophy of a pdxB deletion strain. ThrB was found to be part of a serendipitous metabolic pathway that produces an intermediate of the pyridoxal 5'-phosphate biosynthesis I pathway, 4-phospho-hydroxy-L-threonine, that lies downstream of PdxB [Kim10a]. The 4-hydroxy-L-threonine kinase activity of ThrB that is required for this pathway had already been identified in vitro [Shames84a]. The pathway diverts 3-phosphohydroxypyruvate from serine biosynthesis [Kim10a].

Translation of ThrA and ThrB is coupled [Little89].

Gene Citations: [Parsot83, Lynn87, Theze74a]

Locations: cytosol

Map Position: [2,801 -> 3,733] (0.06 centisomes, 0°)
Length: 933 bp / 310 aa

Molecular Weight of Polypeptide: 33.624 kD (from nucleotide sequence), 29 kD (experimental) [Burr76 ]

Molecular Weight of Multimer: 60.0 kD (experimental) [Burr76]

Unification Links: ASAP:ABE-0000010 , CGSC:110 , EchoBASE:EB0992 , EcoGene:EG10999 , EcoliWiki:b0003 , ModBase:P00547 , OU-Microarray:b0003 , PortEco:thrB , PR:PRO_000024067 , Pride:P00547 , Protein Model Portal:P00547 , RefSeq:NP_414544 , RegulonDB:EG10999 , SMR:P00547 , String:511145.b0003 , UniProt:P00547

Relationship Links: InterPro:IN-FAMILY:IPR000870 , InterPro:IN-FAMILY:IPR006203 , InterPro:IN-FAMILY:IPR006204 , InterPro:IN-FAMILY:IPR013750 , InterPro:IN-FAMILY:IPR014721 , InterPro:IN-FAMILY:IPR020568 , Pfam:IN-FAMILY:PF00288 , Pfam:IN-FAMILY:PF08544 , Prints:IN-FAMILY:PR00958 , Prosite:IN-FAMILY:PS00627

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for thrB

GO Terms:

Biological Process: GO:0009088 - threonine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, Theze74a, Theze74]
GO:0006566 - threonine metabolic process Inferred by computational analysis [GOA01a]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004413 - homoserine kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Burr76]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids threonine

Essentiality data for thrB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 2]
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 1]
No [Feist07, Comment 3]

Curated 13-Mar-2006 by Shearer A , SRI International
Last-Curated ? 08-Dec-2010 by Keseler I , SRI International

Enzymatic reaction of: homoserine kinase

Synonyms: ATP:L-homoserine O-phosphotransferase

EC Number:

L-homoserine + ATP <=> O-phospho-L-homoserine + ADP + 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. [Burr76]

Alternative Substrates for L-homoserine: L-aspartate-semialdehyde [Shames84 , Huo96a ]

In Pathways: aspartate superpathway , superpathway of L-lysine, L-threonine and L-methionine biosynthesis I , superpathway of L-threonine biosynthesis , L-threonine biosynthesis

Cofactors or Prosthetic Groups: K+ [Theze74b], Mg2+ [Burr76, Theze74b]

Cofactor Binding Comment: Mg facilitates binding of homoserine

Inhibitors (Competitive): 2-aminobutanoate [Theze74b, Burr76] , 2-chloro-L-alanine [Theze74b, Burr76] , L-cysteine [Theze74b, Burr76, Comment 4] , L-homocysteine [Theze74b, Burr76, Comment 4] , L-threonine [Theze74b, Burr76, Comment 4]

Inhibitors (Noncompetitive): L-lysine [Chassagnole01]

Inhibitors (Other): L-homoserine [Shames84]

Primary Physiological Regulators of Enzyme Activity: L-threonine

Kinetic Parameters:

Km (μM)

pH(opt): 7.8 [Theze74b]

Enzymatic reaction of: 4-hydroxythreonine kinase (homoserine kinase)

EC Number: 2.7.1.-

4-hydroxy-L-threonine + ATP <=> 4-phospho-hydroxy-L-threonine + ADP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Kinetic Parameters:

Km (μM)

Sequence Features

Protein sequence of ThrB with features indicated

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 91 -> 101
UniProt: ATP; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 139
[Huo96a, UniProt11]
UniProt: 35-fold decrease in kinase activity.
Mutagenesis-Variant 203
[Huo96a, UniProt11]
UniProt: 2-fold decrease in kinase activity but nearly no change in substrates affinity.
Mutagenesis-Variant 206
[Huo96a, UniProt11]
UniProt: 3500-fold decrease in kinase activity.
Mutagenesis-Variant 235
[Huo96a, UniProt11]
[Huo96a, UniProt11]
R → H: 250-fold decrease in kinase activity but no change in substrates affinity.
R → L: 26200-fold decrease in catalytic efficiency.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b0003 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10999; 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

Burr76: Burr B, Walker J, Truffa-Bachi P, Cohen GN (1976). "Homoserine kinase from Escherichia coli K12." Eur J Biochem 1976;62(3);519-26. PMID: 177283

Chassagnole01: Chassagnole C, Rais B, Quentin E, Fell DA, Mazat JP (2001). "An integrated study of threonine-pathway enzyme kinetics in Escherichia coli." Biochem J 356(Pt 2);415-23. PMID: 11368768

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

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."

Huo96: Huo X, Viola RE (1996). "Functional group characterization of homoserine kinase from Escherichia coli." Arch Biochem Biophys 330(2);373-9. PMID: 8660667

Huo96a: Huo X, Viola RE (1996). "Substrate specificity and identification of functional groups of homoserine kinase from Escherichia coli." Biochemistry 35(50);16180-5. PMID: 8973190

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

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

Kim10a: Kim J, Kershner JP, Novikov Y, Shoemaker RK, Copley SD (2010). "Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis." Mol Syst Biol 6;436. PMID: 21119630

Little89: Little S, Hyde S, Campbell CJ, Lilley RJ, Robinson MK (1989). "Translational coupling in the threonine operon of Escherichia coli K-12." J Bacteriol 171(6);3518-22. PMID: 2542227

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Lynn87: Lynn SP, Burton WS, Donohue TJ, Gould RM, Gumport RI, Gardner JF (1987). "Specificity of the attenuation response of the threonine operon of Escherichia coli is determined by the threonine and isoleucine codons in the leader transcript." J Mol Biol 194(1);59-69. PMID: 3112412

Parsot83: Parsot C, Cossart P, Saint-Girons I, Cohen GN (1983). "Nucleotide sequence of thrC and of the transcription termination region of the threonine operon in Escherichia coli K12." Nucleic Acids Res 11(21);7331-45. PMID: 6316258

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

Shames84: Shames SL, Wedler FC (1984). "Homoserine kinase of Escherichia coli: kinetic mechanism and inhibition by L-aspartate semialdehyde." Arch Biochem Biophys 235(2);359-70. PMID: 6097184

Shames84a: Shames SL, Ash DE, Wedler FC, Villafranca JJ (1984). "Interaction of aspartate and aspartate-derived antimetabolites with the enzymes of the threonine biosynthetic pathway of Escherichia coli." J Biol Chem 1984;259:15331-15339. PMID: 6150934

Theze74: Theze J, Margarita D, Cohen GN, Borne F, Patte JC (1974). "Mapping of the structural genes of the three aspartokinases and of the two homoserine dehydrogenases of Escherichia coli K-12." J Bacteriol 117(1);133-43. PMID: 4148765

Theze74a: Theze J, Saint-Girons I (1974). "Threonine locus of Escherichia coli K-12: genetic structure and evidence for an operon." J Bacteriol 118(3);990-8. PMID: 4364333

Theze74b: Theze J, Kleidman L, St Girons I (1974). "Homoserine kinase from Escherichia coli K-12: properties, inhibition by L-threonine, and regulation of biosynthesis." J Bacteriol 1974;118(2);577-81. PMID: 4364023

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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."

Zhao96a: Zhao G, Winkler ME (1996). "4-Phospho-hydroxy-L-threonine is an obligatory intermediate in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12." FEMS Microbiol Lett 1996;135(2-3);275-80. PMID: 8595869

Other References Related to Gene Regulation

Freundlich63: Freundlich M (1963). "Multivalent repression in the biosynthesis of threonine in Salmonella typhimurium and Escherichia coli." Biochem Biophys Res Commun 10;277-82. PMID: 13959617

Gardner79: Gardner JF (1979). "Regulation of the threonine operon: tandem threonine and isoleucine codons in the control region and translational control of transcription termination." Proc Natl Acad Sci U S A 76(4);1706-10. PMID: 287010

Gardner82: Gardner JF (1982). "Initiation, pausing, and termination of transcription in the threonine operon regulatory region of Escherichia coli." J Biol Chem 1982;257(7);3896-904. PMID: 6277952

Lee12a: Lee JH, Lennon CW, Ross W, Gourse RL (2012). "Role of the coiled-coil tip of Escherichia coli DksA in promoter control." J Mol Biol 416(4);503-17. PMID: 22200485

Lynn82: Lynn SP, Gardner JF, Reznikoff WS (1982). "Attenuation regulation in the thr operon of Escherichia coli K-12: molecular cloning and transcription of the controlling region." J Bacteriol 152(1);363-71. PMID: 6811557

Lynn85: Lynn SP, Bauer CE, Chapman K, Gardner JF (1985). "Identification and characterization of mutants affecting transcription termination at the threonine operon attenuator." J Mol Biol 183(4);529-41. PMID: 2410621

Yang91: Yang MT, Gardner JF (1991). "Isolation and footprint analysis of the Escherichia coli thr leader paused transcription complex." Nucleic Acids Res 19(7);1671-80. PMID: 1709279

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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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