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Protein

Thymidylate kinase

Gene

tmk

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth.

Catalytic activityi

ATP + dTMP = ADP + dTDP.

Kineticsi

  1. KM=0.04 mM for ATP (at pH 7.4 and 30 degrees Celsius)1 Publication
  2. KM=15 µM for dTMP (at pH 7.4 and 30 degrees Celsius)1 Publication
  1. Vmax=50 µmol/min/mg enzyme with ATP and dTMP as substrates (at pH 7.4 and 30 degrees Celsius)1 Publication

Pathwayi: dTTP biosynthesis

This protein is involved in the pathway dTTP biosynthesis, which is part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the pathway dTTP biosynthesis and in Pyrimidine metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei12 – 121TMP
Binding sitei74 – 741TMP
Binding sitei78 – 781TMP
Binding sitei100 – 1001TMP
Binding sitei105 – 1051TMP
Binding sitei108 – 1081TMP
Binding sitei109 – 1091TMP
Sitei153 – 1531Transition state stabilizerSequence analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 178ATP

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • thymidylate kinase activity Source: EcoCyc
  • uridylate kinase activity Source: GO_Central

GO - Biological processi

  • dTDP biosynthetic process Source: EcoliWiki
  • dTTP biosynthetic process Source: EcoliWiki
  • dUDP biosynthetic process Source: GO_Central
  • nucleobase-containing small molecule interconversion Source: EcoliWiki
  • nucleotide phosphorylation Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Nucleotide biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:DTMPKI-MONOMER.
ECOL316407:JW1084-MONOMER.
MetaCyc:DTMPKI-MONOMER.
UniPathwayiUPA00575.

Names & Taxonomyi

Protein namesi
Recommended name:
Thymidylate kinase (EC:2.7.4.9)
Alternative name(s):
Thymidine monophosphate kinase
dTMP kinase
Short name:
TMPK
Gene namesi
Name:tmk
Synonyms:ycfG
Ordered Locus Names:b1098, JW1084
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12302. tmk.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: EcoliWiki
  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 213213Thymidylate kinasePRO_0000155269Add
BLAST

Proteomic databases

PaxDbiP0A720.
PRIDEiP0A720.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi4263411. 36 interactions.
DIPiDIP-48110N.
IntActiP0A720. 8 interactions.
MINTiMINT-1258134.
STRINGi511145.b1098.

Structurei

Secondary structure

1
213
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 106Combined sources
Helixi16 – 2914Combined sources
Beta strandi35 – 417Combined sources
Helixi45 – 5511Combined sources
Turni57 – 626Combined sources
Helixi67 – 8418Combined sources
Helixi86 – 916Combined sources
Beta strandi95 – 995Combined sources
Helixi102 – 1087Combined sources
Turni109 – 1135Combined sources
Helixi117 – 12812Combined sources
Beta strandi134 – 1407Combined sources
Helixi143 – 15311Combined sources
Turni158 – 1614Combined sources
Helixi164 – 17916Combined sources
Beta strandi184 – 1885Combined sources
Helixi193 – 20917Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1E9FX-ray1.90A151-156[»]
4TMKX-ray1.98A1-213[»]
5TMPX-ray1.98A1-213[»]
ProteinModelPortaliP0A720.
SMRiP0A720. Positions 2-211.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A720.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni147 – 15913LIDAdd
BLAST

Domaini

The LID domain is a solvent-exposed domain that closes over the site of phosphoryl transfer upon ATP binding.

Sequence similaritiesi

Belongs to the thymidylate kinase family.Curated

Phylogenomic databases

eggNOGiENOG4108ZMD. Bacteria.
COG0125. LUCA.
HOGENOMiHOG000229078.
InParanoidiP0A720.
KOiK00943.
OMAiGGIDIAE.
OrthoDBiEOG64JFSH.
PhylomeDBiP0A720.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00165. Thymidylate_kinase.
InterProiIPR027417. P-loop_NTPase.
IPR018095. Thymidylate_kin_CS.
IPR018094. Thymidylate_kinase.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00041. DTMP_kinase. 1 hit.
PROSITEiPS01331. THYMIDYLATE_KINASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A720-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRSKYIVIEG LEGAGKTTAR NVVVETLEQL GIRDMVFTRE PGGTQLAEKL
60 70 80 90 100
RSLVLDIKSV GDEVITDKAE VLMFYAARVQ LVETVIKPAL ANGTWVIGDR
110 120 130 140 150
HDLSTQAYQG GGRGIDQHML ATLRDAVLGD FRPDLTLYLD VTPEVGLKRA
160 170 180 190 200
RARGELDRIE QESFDFFNRT RARYLELAAQ DKSIHTIDAT QPLEAVMDAI
210
RTTVTHWVKE LDA
Length:213
Mass (Da):23,783
Last modified:March 15, 2005 - v1
Checksum:i16BC0A725AAFCB72
GO

Sequence cautioni

The sequence L01483 differs from that shown. Reason: Frameshift at positions 92 and 136. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti112 – 1121G → A (PubMed:8509334).Curated
Sequence conflicti122 – 1221T → N (PubMed:8509334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U41456 Genomic DNA. Translation: AAB06878.1.
U00096 Genomic DNA. Translation: AAC74182.1.
AP009048 Genomic DNA. Translation: BAA35905.1.
L01483 Genomic DNA. No translation available.
L04577 Genomic DNA. No translation available.
PIRiJC6006. G64853.
RefSeqiNP_415616.1. NC_000913.3.
WP_001257000.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74182; AAC74182; b1098.
BAA35905; BAA35905; BAA35905.
GeneIDi945663.
KEGGiecj:JW1084.
eco:b1098.
PATRICi32117437. VBIEscCol129921_1141.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U41456 Genomic DNA. Translation: AAB06878.1.
U00096 Genomic DNA. Translation: AAC74182.1.
AP009048 Genomic DNA. Translation: BAA35905.1.
L01483 Genomic DNA. No translation available.
L04577 Genomic DNA. No translation available.
PIRiJC6006. G64853.
RefSeqiNP_415616.1. NC_000913.3.
WP_001257000.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1E9FX-ray1.90A151-156[»]
4TMKX-ray1.98A1-213[»]
5TMPX-ray1.98A1-213[»]
ProteinModelPortaliP0A720.
SMRiP0A720. Positions 2-211.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263411. 36 interactions.
DIPiDIP-48110N.
IntActiP0A720. 8 interactions.
MINTiMINT-1258134.
STRINGi511145.b1098.

Proteomic databases

PaxDbiP0A720.
PRIDEiP0A720.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74182; AAC74182; b1098.
BAA35905; BAA35905; BAA35905.
GeneIDi945663.
KEGGiecj:JW1084.
eco:b1098.
PATRICi32117437. VBIEscCol129921_1141.

Organism-specific databases

EchoBASEiEB2208.
EcoGeneiEG12302. tmk.

Phylogenomic databases

eggNOGiENOG4108ZMD. Bacteria.
COG0125. LUCA.
HOGENOMiHOG000229078.
InParanoidiP0A720.
KOiK00943.
OMAiGGIDIAE.
OrthoDBiEOG64JFSH.
PhylomeDBiP0A720.

Enzyme and pathway databases

UniPathwayiUPA00575.
BioCyciEcoCyc:DTMPKI-MONOMER.
ECOL316407:JW1084-MONOMER.
MetaCyc:DTMPKI-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A720.
PROiP0A720.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00165. Thymidylate_kinase.
InterProiIPR027417. P-loop_NTPase.
IPR018095. Thymidylate_kin_CS.
IPR018094. Thymidylate_kinase.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00041. DTMP_kinase. 1 hit.
PROSITEiPS01331. THYMIDYLATE_KINASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Escherichia coli thymidylate kinase: molecular cloning, nucleotide sequence, and genetic organization of the corresponding tmk locus."
    Reynes J.-P., Tiraby M., Baron M., Drocourt D., Tiraby G.
    J. Bacteriol. 178:2804-2812(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Identification, isolation, and characterization of the structural gene encoding the delta' subunit of Escherichia coli DNA polymerase III holoenzyme."
    Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S.
    J. Bacteriol. 175:3812-3822(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 85-213.
    Strain: K12 / MG1655 / ATCC 47076.
  6. "DNA polymerase III accessory proteins. I. holA and holB encoding delta and delta'."
    Dong Z., Onrust R., Skangalis M., O'Donnell M.
    J. Biol. Chem. 268:11758-11765(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 162-213.
    Strain: K12.
  7. "Thymidylate kinase of Mycobacterium tuberculosis: a chimera sharing properties common to eukaryotic and bacterial enzymes."
    Munier-Lehmann H., Chaffotte A., Pochet S., Labesse G.
    Protein Sci. 10:1195-1205(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: KINETIC PARAMETERS.
  8. "Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase."
    Lavie A., Ostermann N., Brundiers R., Goody R.S., Reinstein J., Konrad M., Schlichting I.
    Proc. Natl. Acad. Sci. U.S.A. 95:14045-14050(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS) OF COMPLEXES WITH THE BISUBSTRATE INHIBITORS TP5A AND AZT-P5A.

Entry informationi

Entry nameiKTHY_ECOLI
AccessioniPrimary (citable) accession number: P0A720
Secondary accession number(s): P37345
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: February 17, 2016
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.