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



Gene: thiM Accession Numbers: M007 (EcoCyc), b2104, ECK2097

Regulation Summary Diagram: ?

Summary:
Hydroxyethylthiazole kinase (ThiM) catalyzes one of two reactions that feed 4-methyl-5-(β-hydroxyethyl)thiazole phosphate into the thiamine biosynthesis pathway. ThiM catalyzes the ATP-dependent phosphorylation of 4-methyl-5-(β-hydroxyethyl)thiazole to generate 4-methyl-5-(β-hydroxyethyl)thiazole phosphate [Mizote89].

thiM mRNA contains a riboswitch that binds to the thiamine biosynthesis pathway product thiamine pyrophosphate (TPP). This interaction has been examined via NMR and a 2.0 Å resolution crystal structure [Noeske06, Serganov06]. The secondary structure of ThiM in its TPP-free and -bound form have been reported [Rentmeister07]. Mutations of conserved bases of the riboswitch domain have been investigated using in vivo expression analysis [OntiverosPalaci08]. The active process of TPP-induced folding of thiM has been directly evaluated via fluorescence spectroscopy [Lang07]. A method to screen for compounds that bind the riboswitch region has been developed and used to study the riboswitch ligand interactions [Chen10c, Chen12b].

Locations: cytosol

Map Position: [2,182,535 <- 2,183,323] (47.04 centisomes)
Length: 789 bp / 262 aa

Molecular Weight of Polypeptide: 27.339 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006960 , EchoBASE:EB3822 , EcoGene:EG14069 , EcoliWiki:b2104 , ModBase:P76423 , OU-Microarray:b2104 , PortEco:thiM , PR:PRO_000024062 , Pride:P76423 , Protein Model Portal:P76423 , RefSeq:NP_416607 , RegulonDB:M007 , SMR:P76423 , String:511145.b2104 , Swiss-Model:P76423 , UniProt:P76423

Relationship Links: InterPro:IN-FAMILY:IPR000417 , Pfam:IN-FAMILY:PF02110 , Prints:IN-FAMILY:PR01099

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009228 - thiamine biosynthetic process Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0009229 - thiamine diphosphate biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004417 - hydroxyethylthiazole kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Mizote89]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers thiamin

Essentiality data for thiM 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:
Curated 19-Sep-2006 by Shearer A , SRI International
Last-Curated ? 05-Aug-2013 by Kubo A , SRI International


Enzymatic reaction of: hydroxyethylthiazole kinase

Synonyms: 4-methyl-5-(β-hydroxyethyl)thiazole kinase, ATP:4-methyl-5-(2-hydroxyethyl)-thiazole 2-phosphotransferase, THZ kinase

EC Number: 2.7.1.50

ATP + 4-methyl-5-(β-hydroxyethyl)thiazole <=> ADP + 4-methyl-5-(2-phosphonooxyethyl)thiazole + 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 physiologically favored in the direction shown.

In Pathways: thiamin salvage II


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 50
[UniProt10]
UniProt: Substrate; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 125
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 171
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 198
[UniProt10]
UniProt: Substrate; via amide nitrogen; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
3/2/1998 (pkarp) Merged genes G7136/thiM and M007/EG14069
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Chen10c: Chen L, Cressina E, Leeper FJ, Smith AG, Abell C (2010). "A fragment-based approach to identifying ligands for riboswitches." ACS Chem Biol 5(4);355-8. PMID: 20158266

Chen12b: Chen L, Cressina E, Dixon N, Erixon K, Agyei-Owusu K, Micklefield J, Smith AG, Abell C, Leeper FJ (2012). "Probing riboswitch-ligand interactions using thiamine pyrophosphate analogues." Org Biomol Chem 10(30);5924-31. PMID: 22514012

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.

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

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

Lang07: Lang K, Rieder R, Micura R (2007). "Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach." Nucleic Acids Res 35(16);5370-8. PMID: 17693433

Mizote89: Mizote T, Nakayama H (1989). "The thiM locus and its relation to phosphorylation of hydroxyethylthiazole in Escherichia coli." J Bacteriol 171(6);3228-32. PMID: 2542220

Noeske06: Noeske J, Richter C, Stirnal E, Schwalbe H, Wohnert J (2006). "Phosphate-group recognition by the aptamer domain of the thiamine pyrophosphate sensing riboswitch." Chembiochem 7(9);1451-6. PMID: 16871614

OntiverosPalaci08: Ontiveros-Palacios N, Smith AM, Grundy FJ, Soberon M, Henkin TM, Miranda-Rios J (2008). "Molecular basis of gene regulation by the THI-box riboswitch." Mol Microbiol 67(4);793-803. PMID: 18179415

Rentmeister07: Rentmeister A, Mayer G, Kuhn N, Famulok M (2007). "Conformational changes in the expression domain of the Escherichia coli thiM riboswitch." Nucleic Acids Res 35(11);3713-22. PMID: 17517779

Serganov06: Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ (2006). "Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch." Nature 441(7097);1167-71. PMID: 16728979

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

Other References Related to Gene Regulation

Edwards06: Edwards TE, Ferre-D'Amare AR (2006). "Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition." Structure 14(9);1459-68. PMID: 16962976

Kulshina10: Kulshina N, Edwards TE, Ferre-D'Amare AR (2010). "Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch." RNA 16(1);186-96. PMID: 19948769

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

MirandaRios07: Miranda-Rios J (2007). "The THI-box riboswitch, or how RNA binds thiamin pyrophosphate." Structure 15(3);259-65. PMID: 17355861

Winkler02: Winkler W, Nahvi A, Breaker RR (2002). "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression." Nature 419(6910);952-6. PMID: 12410317


Report Errors or Provide Feedback
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 Wed Nov 26, 2014, biocyc13.