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



Gene: tmk Accession Numbers: EG12302 (EcoCyc), b1098, ECK1084

Synonyms: ycfG

Regulation Summary Diagram: ?

Summary:
The enzyme is responsible for specifically catalyzing the conversion of dTMP to dTDP. [Daws84]

dTMP kinase is the last unique enzyme in the pathway leading to dTTP. [Daws84]

Thymidylate kinase is essential for growth [Chaperon06].

Locations: cytosol

Map Position: [1,154,347 -> 1,154,988] (24.88 centisomes)
Length: 642 bp / 213 aa

Molecular Weight of Polypeptide: 23.783 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003714 , DIP:DIP-48110N , EchoBASE:EB2208 , EcoGene:EG12302 , EcoliWiki:b1098 , Mint:MINT-1258134 , ModBase:P0A720 , OU-Microarray:b1098 , PortEco:tmk , Pride:P0A720 , Protein Model Portal:P0A720 , RefSeq:NP_415616 , RegulonDB:EG12302 , SMR:P0A720 , String:511145.b1098 , UniProt:P0A720

Relationship Links: InterPro:IN-FAMILY:IPR018094 , InterPro:IN-FAMILY:IPR018095 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR10344 , PDB:Structure:1E9F , PDB:Structure:4TMK , PDB:Structure:5TMP , Pfam:IN-FAMILY:PF02223 , Prosite:IN-FAMILY:PS01331

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006233 - dTDP biosynthetic process Inferred from experiment Inferred by computational analysis [GOA01a, Reynes96]
GO:0006235 - dTTP biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA06, Reynes96, Daws84]
GO:0015949 - nucleobase-containing small molecule interconversion Inferred from experiment [Reynes96]
GO:0046939 - nucleotide phosphorylation Inferred by computational analysis Inferred from experiment [Reynes96, Daws84, GOA06, GOA01, GOA01a]
GO:0009165 - nucleotide biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004798 - thymidylate kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Reynes96, Daws84]
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:0005737 - cytoplasm Inferred from experiment [Reynes96]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for tmk knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Credits:
Last-Curated ? 24-Mar-2008 by Fulcher C , SRI International


Enzymatic reaction of: dTMP kinase

Synonyms: thymidylate kinase

EC Number: 2.7.4.9/2.7.4.12/2.7.4.13

dTMP + ATP <=> dTDP + ADP

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 dTMP [Comment 2 ]: 5-iodo-2'-dUMP , dUMP

In Pathways: superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli) , superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis , pyrimidine deoxyribonucleotides de novo biosynthesis I , pyrimidine deoxyribonucleotide phosphorylation , pyrimidine deoxyribonucleotides de novo biosynthesis II

Summary:
The enzyme is responsible for specifically catalyzing the conversion of dTMP to dTDP. [Daws84]

dTMP kinase activity has been assayed in ether-permeabilized cells of a derivative of Escherichia coli K-12. A mutant was isolated from this strain which had a 25-fold lower specific activity and a 5-fold higher Km for dTMP [Daws84]. The enzyme has been purified and characterized from Escherichia coli B [Nelson69].

Cofactors or Prosthetic Groups: Mg2+ [Comment 3]

Inhibitors (Competitive): 5-iodo-2'-dUMP [Nelson69, Helmward89] , dUMP [Nelson69, Helmward89]

Inhibitors (Unknown Mechanism): dTTP [Nelson69, Helmward89, Comment 4] , dCTP [Helmward89, Nelson69, Comment 4] , ATP [Nelson69, Helmward89, Comment 4] , ammonium [Helmward89] , Na+ [Helmward89] , K+ [Helmward89]

Kinetic Parameters:

Substrate
Km (μM)
Citations
ATP
40.0
[Tourneux98, BRENDA14]
ATP
1200.0
[Nelson69, BRENDA14]
dTMP
240.0
[Nelson69, BRENDA14]
dTMP
15.0
[Tourneux98, BRENDA14]

pH(opt): 7.8 [BRENDA14, Nelson69]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 10 -> 17
[UniProt10]
UniProt: ATP;
Amino-Acid-Sites-That-Bind 12
[UniProt10]
UniProt: TMP;
Amino-Acid-Sites-That-Bind 74
[UniProt10]
UniProt: TMP;
Amino-Acid-Sites-That-Bind 78
[UniProt10]
UniProt: TMP;
Amino-Acid-Sites-That-Bind 100
[UniProt10]
UniProt: TMP;
Amino-Acid-Sites-That-Bind 105
[UniProt10]
UniProt: TMP;
Amino-Acid-Sites-That-Bind 108
[UniProt10]
UniProt: TMP;
Amino-Acid-Sites-That-Bind 109
[UniProt10]
UniProt: TMP;
Sequence-Conflict 112
[Carter93, UniProt10]
Alternate sequence: G → A; UniProt: (in Ref. 5);
Sequence-Conflict 122
[Carter93, UniProt10]
Alternate sequence: T → N; UniProt: (in Ref. 5);
Protein-Segment 147 -> 159
[UniProt10a]
UniProt: LID; Sequence Annotation Type: region of interest;
Amino-Acid-Site 153
[UniProt10a]
UniProt: Transition state stabilizer; Sequence Annotation Type: site; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
3/2/1998 (pkarp) Merged genes G157/EG12302 and EG12302/tmk
1/26/1998 (pkarp) Merged genes G7998/tmk and EG12302/ycfG


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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Carter93: Carter JR, Franden MA, Aebersold R, McHenry CS (1993). "Identification, isolation, and characterization of the structural gene encoding the delta' subunit of Escherichia coli DNA polymerase III holoenzyme." J Bacteriol 175(12);3812-22. PMID: 8509334

Chaperon06: Chaperon DN (2006). "Construction and complementation of in-frame deletions of the essential Escherichia coli thymidylate kinase gene." Appl Environ Microbiol 72(2);1288-94. PMID: 16461678

Daws84: Daws TD, Fuchs JA (1984). "Isolation and characterization of an Escherichia coli mutant deficient in dTMP kinase activity." J Bacteriol 1984;157(2);440-4. PMID: 6319360

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

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."

Helmward89: Helmward Z "Handbook of Enzyme Inhibitors. 2nd, revised and enlarged edition." Weinheim, Federal Republic of Germany ; New York, NY, USA , 1989.

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

Nelson69: Nelson DJ, Carter CE (1969). "Purification and characterization of Thymidine 5-monophosphate kinase from Escherichia coli B." J Biol Chem 1969;244(19);5254-62. PMID: 4899016

Reynes96: Reynes JP, Tiraby M, Baron M, Drocourt D, Tiraby G (1996). "Escherichia coli thymidylate kinase: molecular cloning, nucleotide sequence, and genetic organization of the corresponding tmk locus." J Bacteriol 178(10);2804-12. PMID: 8631667

Tourneux98: Tourneux L, Bucurenci N, Lascu I, Sakamoto H, Briand G, Gilles AM (1998). "Substitution of an alanine residue for glycine 146 in TMP kinase from Escherichia coli is responsible for bacterial hypersensitivity to bromodeoxyuridine." J Bacteriol 180(16);4291-3. PMID: 9696781

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

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

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."


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 Dec 17, 2014, biocyc13.