O05891 (KTHY_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Thymidylate kinase
EC=2.7.4.9

Alternative name(s):
Thymidine monophosphate kinase
dTMP kinase
Short name=TMPK

Gene names

Name:	tmk
Ordered Locus Names:	Rv3247c, MT3345

Organism

Mycobacterium tuberculosis

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex

Protein attributes

Sequence length	214 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with ITP, GTP, CTP and UTP. HAMAP MF_00165
Catalytic activity	ATP + dTMP = ADP + dTDP. HAMAP MF_00165
Cofactor	Binds 1 magnesium ion per subunit. This ion is required for catalysis, binding to the active site transiently (at the TMP-binding site), and probably acting as a clamp between the phosphoryl donor and acceptor.
Enzyme regulation	Competitively inhibited at the phosphate acceptor site by 3'-azido-3'-deoxythymidine monophosphate (AZT-MP) (in contrast to other TMPKs such as E.coli, in which it is a good substrate). Inhibition seems to result from the impossibility of magnesium binding. HAMAP MF_00165
Pathway	Pyrimidine metabolism; dTTP biosynthesis. HAMAP MF_00165
Subunit structure	Homodimer. Ref.3
Domain	The LID domain is a solvent-exposed domain that closes over the site of phosphoryl transfer upon ATP binding. HAMAP MF_00165
Miscellaneous	Was identified as a high-confidence drug target. HAMAP MF_00165
Sequence similarities	Belongs to the thymidylate kinase family.
Biophysicochemical properties	Kinetic parameters: KM=0.1 mM for ATP (at pH 7.4 and 30 degrees Celsius) Ref.3 KM=4.5 µM for dTMP (at pH 7.4 and 30 degrees Celsius) KM=0.14 mM for dehydro-TMP (at pH 7.4 and 30 degrees Celsius) KM=2.10 mM for dUMP (at pH 7.4 and 30 degrees Celsius) Vmax=13 µmol/min/mg enzyme with ATP and dTMP as substrates (at pH 7.4 and 30 degrees Celsius) Vmax=0.16 µmol/min/mg enzyme with ATP and dehydro-TMP as substrates (at pH 7.4 and 30 degrees Celsius) Vmax=3.50 µmol/min/mg enzyme with ATP and dUMP as substrates (at pH 7.4 and 30 degrees Celsius) pH dependence: Optimum pH is 7.5-8.5. Inactive below pH 4.6. Temperature dependence: Highly thermostable. Is half-inactivated at 65 degrees Celsius.
Mass spectrometry	Molecular mass is 22635.89±2.23 Da from positions 1 - 214. Determined by ESI. Ref.3

Ontologies

Keywords
Biological process	Nucleotide biosynthesis
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	TMP metabolic process Inferred from direct assay Ref.6. Source: MTBBASE dTDP biosynthetic process Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from direct assay Ref.3. Source: MTBBASE GTP binding Inferred from direct assay Ref.3. Source: MTBBASE magnesium ion binding Inferred from direct assay Ref.6. Source: MTBBASE protein homodimerization activity Inferred from physical interaction Ref.3. Source: MTBBASE thymidylate kinase activity Inferred from direct assay Ref.3. Source: MTBBASE
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 214

214

Thymidylate kinase HAMAP MF_00165

PRO_0000155309

Regions

Nucleotide binding

7 – 14

8

ATP HAMAP MF_00165

Region

147 – 159

13

LID HAMAP MF_00165

Sites

Metal binding

9

1

Magnesium

Metal binding

166

1

Magnesium

Binding site

9

1

TMP

Binding site

39

1

TMP

Binding site

70

1

TMP

Binding site

74

1

TMP

Binding site

95

1

TMP

Binding site

100

1

TMP

Binding site

103

1

TMP

Binding site

163

1

TMP

Binding site

165

1

TMP

Site

153

1

Transition state stabilizer Potential

Secondary structure

1

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214

Helix Strand Turn

Details...

Beta strand

2 – 6

5

Helix

13 – 26

14

Beta strand

31 – 37

7

Turn

39 – 41

3

Helix

43 – 52

10

Helix

59 – 61

3

Helix

63 – 75

13

Helix

78 – 87

10

Beta strand

89 – 95

7

Helix

97 – 107

11

Helix

115 – 124

10

Turn

125 – 127

3

Beta strand

134 – 139

6

Helix

143 – 156

14

Helix

158 – 160

3

Turn

164 – 167

4

Helix

169 – 185

17

Turn

186 – 188

3

Beta strand

189 – 194

6

Helix

200 – 207

8

Sequences

	Sequence		Length	Mass (Da)
	O05891 [UniParc]. Last modified July 1, 1997. Version 1. Checksum: E435123C250F46E7	FASTA	214	22,635
	10 20 30 40 50 60 MLIAIEGVDG AGKRTLVEKL SGAFRAAGRS VATLAFPRYG QSVAADIAAE ALHGEHGDLA 70 80 90 100 110 120 SSVYAMATLF ALDRAGAVHT IQGLCRGYDV VILDRYVASN AAYSAARLHE NAAGKAAAWV 130 140 150 160 170 180 QRIEFARLGL PKPDWQVLLA VSAELAGERS RGRAQRDPGR ARDNYERDAE LQQRTGAVYA 190 200 210 ELAAQGWGGR WLVVGADVDP GRLAATLAPP DVPS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence." Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K. , Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S., Barrell B.G. Nature 393:537-544(1998) [PubMed: 9634230] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 25618 / H37Rv.
[2]	"Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains." Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L., Delcher A., Utterback T.R. , Weidman J.F., Khouri H.M., Gill J., Mikula A., Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M. J. Bacteriol. 184:5479-5490(2002) [PubMed: 12218036] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CDC 1551 / Oshkosh.
[3]	"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: 11369858] [Abstract] Cited for: PROTEIN SEQUENCE OF N-TERMINUS, PARTIAL PROTEIN SEQUENCE, CHARACTERIZATION, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, MASS SPECTROMETRY. Strain: ATCC 25618 / H37Rv.
[4]	"Crystallization and preliminary X-ray analysis of the thymidylate kinase from Mycobacterium tuberculosis." Li de la Sierra I., Munier-Lehmann H., Gilles A.-M., Barzu O., Delarue M. Acta Crystallogr. D 56:226-228(2000) [PubMed: 10666613] [Abstract] Cited for: CRYSTALLIZATION.
[5]	"targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis." Raman K., Yeturu K., Chandra N. BMC Syst. Biol. 2:109-109(2008) [PubMed: 19099550] [Abstract] Cited for: IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
[6]	"X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution." Li de la Sierra I., Munier-Lehmann H., Gilles A.-M., Barzu O., Delarue M. J. Mol. Biol. 311:87-100(2001) [PubMed: 11469859] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF COMPLEX WITH THYMIDINE MONOPHOSPHATE.
[7]	"Cryophotolysis of caged compounds: a technique for trapping intermediate states in protein crystals." Ursby T., Weik M., Fioravanti E., Delarue M., Goeldner M., Bourgeois D. Acta Crystallogr. D 58:607-614(2002) [PubMed: 11914484] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF COMPLEXES WITH THYMIDINE MONOPHOSPHATE AND THYMIDINE-5'-DIPHOSPHATE.
[8]	"Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism." Haouz A., Vanheusden V., Munier-Lehmann H., Froeyen M., Herdewijn P., Van Calenbergh S., Delarue M. J. Biol. Chem. 278:4963-4971(2003) [PubMed: 12454011] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF COMPLEXES WITH THE INHIBITORS AP5T AND 5-CH2OH DEOXYURIDINE MONOPHOSPHATE.
[9]	"Mycobacterium tuberculosis thymidylate kinase: structural studies of intermediates along the reaction pathway." Fioravanti E., Haouz A., Ursby T., Munier-Lehmann H., Delarue M., Bourgeois D. J. Mol. Biol. 327:1077-1092(2003) [PubMed: 12662932] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEXES WITH THYMIDINE MONOPHOSPHATE, THYMIDINE DIPHOSPHATE AND THYMIDINE TRIPHOSPHATE, PH DEPENDENCE, ROLE OF THE MAGNESIUM ION.
[10]	"The crystal structure of Mycobacterium tuberculosis thymidylate kinase in complex with 3'-azidodeoxythymidine monophosphate suggests a mechanism for competitive inhibition." Fioravanti E., Adam V., Munier-Lehmann H., Bourgeois D. Biochemistry 44:130-137(2005) [PubMed: 15628853] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF COMPLEXES WITH DEOXYTHYMIDINE AND AZIDODEOXYTHYMIDINE MONOPHOSPHATE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BX842582 Genomic DNA. Translation: CAB08348.1.
AE000516 Genomic DNA. Translation: AAK47687.1.

PIR

A70593.

RefSeq

NP_217764.1. NC_000962.2.
NP_337873.1. NC_002755.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1G3U	X-ray	1.95	A	1-214	[»]
1GSI	X-ray	1.60	A	1-214	[»]
1GTV	X-ray	1.55	A/B	1-214	[»]
1MRN	X-ray	2.45	A	1-214	[»]
1MRS	X-ray	2.00	A	1-214	[»]
1N5I	X-ray	1.85	A	1-214	[»]
1N5J	X-ray	1.85	A	1-214	[»]
1N5K	X-ray	2.10	A/B	1-214	[»]
1N5L	X-ray	2.30	A/B	1-214	[»]
1W2G	X-ray	2.10	A/B	1-214	[»]
1W2H	X-ray	2.00	A/B	1-214	[»]

ProteinModelPortal

O05891.

SMR

O05891. Positions 1-208.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBMYCT00000002222; EBMYCP00000002222; EBMYCG00000002220.
EBMYCT00000070858; EBMYCP00000068917; EBMYCG00000070853.

GeneID

888740.
923013.

GenomeReviews

Gene locus MT3345 in contig AE000516_GR.
Gene locus Rv3247c in contig AL123456_GR.

KEGG

mtc:MT3345.
mtu:Rv3247c.

PATRIC

18129110. VBIMycTub22151_3651.

TIGR

MT3345.

Organism-specific databases

TubercuList

Rv3247c.

Phylogenomic databases

GeneTree

EBGT00050000016314.

HOGENOM

HBG626009.

OMA

FPRYGRS.

ProtClustDB

PRK07933.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-15785.

Family and domain databases

HAMAP

MF_00165. Thymidylate_kinase.
[Tree]

InterPro

IPR018095. Thymidylate_kin_CS.
IPR018094. Thymidylate_kinase.
[Graphical view]

KO

K00943.

Pfam

PF02223. Thymidylate_kin. 1 hit.
[Graphical view]

PROSITE

PS01331. THYMIDYLATE_KINASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

KTHY_MYCTU

Accession

Primary (citable) accession number: O05891
Secondary accession number(s): Q7D5U8

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2005
Last sequence update:	July 1, 1997
Last modified:	January 25, 2012
This is version 81 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program