KTHY_MYCTU
ID KTHY_MYCTU Reviewed; 214 AA.
AC P9WKE1; L0TDK8; O05891; Q7D5U8;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 47.
DE RecName: Full=Thymidylate kinase {ECO:0000303|PubMed:11369858};
DE EC=2.7.4.9 {ECO:0000269|PubMed:11369858};
DE AltName: Full=Thymidine monophosphate kinase;
DE AltName: Full=dTMP kinase;
DE Short=TMPK;
GN Name=tmk; OrderedLocusNames=Rv3247c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP PROTEIN SEQUENCE OF N-TERMINUS, PARTIAL PROTEIN SEQUENCE, FUNCTION,
RP CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, AND MASS SPECTROMETRY.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=11369858; DOI=10.1110/ps.45701;
RA Munier-Lehmann H., Chaffotte A., Pochet S., Labesse G.;
RT "Thymidylate kinase of Mycobacterium tuberculosis: a chimera sharing
RT properties common to eukaryotic and bacterial enzymes.";
RL Protein Sci. 10:1195-1205(2001).
RN [3]
RP CRYSTALLIZATION.
RX PubMed=10666613; DOI=10.1107/s0907444999016212;
RA Li de la Sierra I., Munier-Lehmann H., Gilles A.-M., Barzu O., Delarue M.;
RT "Crystallization and preliminary X-ray analysis of the thymidylate kinase
RT from Mycobacterium tuberculosis.";
RL Acta Crystallogr. D 56:226-228(2000).
RN [4]
RP IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
RX PubMed=19099550; DOI=10.1186/1752-0509-2-109;
RA Raman K., Yeturu K., Chandra N.;
RT "targetTB: a target identification pipeline for Mycobacterium tuberculosis
RT through an interactome, reactome and genome-scale structural analysis.";
RL BMC Syst. Biol. 2:109-109(2008).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF COMPLEX WITH THYMIDINE
RP MONOPHOSPHATE.
RX PubMed=11469859; DOI=10.1006/jmbi.2001.4843;
RA Li de la Sierra I., Munier-Lehmann H., Gilles A.-M., Barzu O., Delarue M.;
RT "X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed
RT with TMP at 1.95 A resolution.";
RL J. Mol. Biol. 311:87-100(2001).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF COMPLEXES WITH THYMIDINE
RP MONOPHOSPHATE AND THYMIDINE-5'-DIPHOSPHATE.
RX PubMed=11914484; DOI=10.1107/s0907444902002135;
RA Ursby T., Weik M., Fioravanti E., Delarue M., Goeldner M., Bourgeois D.;
RT "Cryophotolysis of caged compounds: a technique for trapping intermediate
RT states in protein crystals.";
RL Acta Crystallogr. D 58:607-614(2002).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF COMPLEXES WITH THE INHIBITORS AP5T
RP AND 5-CH2OH DEOXYURIDINE MONOPHOSPHATE.
RX PubMed=12454011; DOI=10.1074/jbc.m209630200;
RA Haouz A., Vanheusden V., Munier-Lehmann H., Froeyen M., Herdewijn P.,
RA Van Calenbergh S., Delarue M.;
RT "Enzymatic and structural analysis of inhibitors designed against
RT Mycobacterium tuberculosis thymidylate kinase. New insights into the
RT phosphoryl transfer mechanism.";
RL J. Biol. Chem. 278:4963-4971(2003).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEXES WITH
RP THYMIDINE MONOPHOSPHATE, THYMIDINE DIPHOSPHATE AND THYMIDINE TRIPHOSPHATE,
RP PH DEPENDENCE, AND ROLE OF THE MAGNESIUM ION.
RX PubMed=12662932; DOI=10.1016/s0022-2836(03)00202-x;
RA Fioravanti E., Haouz A., Ursby T., Munier-Lehmann H., Delarue M.,
RA Bourgeois D.;
RT "Mycobacterium tuberculosis thymidylate kinase: structural studies of
RT intermediates along the reaction pathway.";
RL J. Mol. Biol. 327:1077-1092(2003).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF COMPLEXES WITH DEOXYTHYMIDINE AND
RP AZIDODEOXYTHYMIDINE MONOPHOSPHATE.
RX PubMed=15628853; DOI=10.1021/bi0484163;
RA Fioravanti E., Adam V., Munier-Lehmann H., Bourgeois D.;
RT "The crystal structure of Mycobacterium tuberculosis thymidylate kinase in
RT complex with 3'-azidodeoxythymidine monophosphate suggests a mechanism for
RT competitive inhibition.";
RL Biochemistry 44:130-137(2005).
CC -!- FUNCTION: Catalyzes the reversible phosphorylation of deoxythymidine
CC monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as
CC its preferred phosphoryl donor. Situated at the junction of both de
CC novo and salvage pathways of deoxythymidine triphosphate (dTTP)
CC synthesis, is essential for DNA synthesis and cellular growth. Has a
CC broad specificity for nucleoside triphosphates, being highly active
CC with ATP or dATP as phosphate donors, and less active with ITP, GTP,
CC CTP and UTP. {ECO:0000269|PubMed:11369858}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + dTMP = ADP + dTDP; Xref=Rhea:RHEA:13517,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:58369, ChEBI:CHEBI:63528,
CC ChEBI:CHEBI:456216; EC=2.7.4.9;
CC Evidence={ECO:0000269|PubMed:11369858};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 1 Mg(2+) ion per subunit. This ion is required for
CC catalysis, binding to the active site transiently (at the TMP-binding
CC site), and probably acting as a clamp between the phosphoryl donor and
CC acceptor.;
CC -!- ACTIVITY REGULATION: Competitively inhibited at the phosphate acceptor
CC site by 3'-azido-3'-deoxythymidine monophosphate (AZT-MP) (in contrast
CC to other TMPKs such as E.coli, in which it is a good substrate).
CC Inhibition seems to result from the impossibility of magnesium binding.
CC {ECO:0000269|PubMed:11369858}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.1 mM for ATP (at pH 7.4 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:11369858};
CC KM=4.5 uM for dTMP (at pH 7.4 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:11369858};
CC KM=0.14 mM for dehydro-TMP (at pH 7.4 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:11369858};
CC KM=2.10 mM for dUMP (at pH 7.4 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:11369858};
CC Vmax=13 umol/min/mg enzyme with ATP and dTMP as substrates (at pH 7.4
CC and 30 degrees Celsius) {ECO:0000269|PubMed:11369858};
CC Vmax=0.16 umol/min/mg enzyme with ATP and dehydro-TMP as substrates
CC (at pH 7.4 and 30 degrees Celsius) {ECO:0000269|PubMed:11369858};
CC Vmax=3.50 umol/min/mg enzyme with ATP and dUMP as substrates (at pH
CC 7.4 and 30 degrees Celsius) {ECO:0000269|PubMed:11369858};
CC pH dependence:
CC Optimum pH is 7.5-8.5. Inactive below pH 4.6.
CC {ECO:0000269|PubMed:11369858, ECO:0000269|PubMed:12662932};
CC Temperature dependence:
CC Highly thermostable. Is half-inactivated at 65 degrees Celsius.
CC {ECO:0000269|PubMed:11369858};
CC -!- PATHWAY: Pyrimidine metabolism; dTTP biosynthesis.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11369858}.
CC -!- DOMAIN: The LID domain is a solvent-exposed domain that closes over the
CC site of phosphoryl transfer upon ATP binding.
CC -!- MASS SPECTROMETRY: Mass=22635.89; Mass_error=2.23; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:11369858};
CC -!- MISCELLANEOUS: Was identified as a high-confidence drug target.
CC -!- SIMILARITY: Belongs to the thymidylate kinase family. {ECO:0000305}.
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DR EMBL; AL123456; CCP46066.1; -; Genomic_DNA.
DR PIR; A70593; A70593.
DR RefSeq; NP_217764.1; NC_000962.3.
DR RefSeq; WP_003417036.1; NZ_NVQJ01000003.1.
DR PDB; 1G3U; X-ray; 1.95 A; A=1-214.
DR PDB; 1GSI; X-ray; 1.60 A; A=1-214.
DR PDB; 1GTV; X-ray; 1.55 A; A/B=1-214.
DR PDB; 1MRN; X-ray; 2.45 A; A=1-214.
DR PDB; 1MRS; X-ray; 2.00 A; A=1-214.
DR PDB; 1N5I; X-ray; 1.85 A; A=1-214.
DR PDB; 1N5J; X-ray; 1.85 A; A=1-214.
DR PDB; 1N5K; X-ray; 2.10 A; A/B=1-214.
DR PDB; 1N5L; X-ray; 2.30 A; A/B=1-214.
DR PDB; 1W2G; X-ray; 2.10 A; A/B=1-214.
DR PDB; 1W2H; X-ray; 2.00 A; A/B=1-214.
DR PDB; 4UNN; X-ray; 2.50 A; A/B=2-214.
DR PDB; 4UNP; X-ray; 2.30 A; A=1-210.
DR PDB; 4UNQ; X-ray; 2.30 A; A/B=1-210.
DR PDB; 4UNR; X-ray; 1.98 A; A/B=1-210.
DR PDB; 4UNS; X-ray; 2.18 A; A/B=1-210.
DR PDB; 5NQ5; X-ray; 2.85 A; A=1-214.
DR PDB; 5NR7; X-ray; 2.35 A; A/B=1-214.
DR PDB; 5NRN; X-ray; 2.20 A; A/B=1-214.
DR PDB; 5NRQ; X-ray; 2.10 A; A/B=1-214.
DR PDB; 6YT1; X-ray; 1.90 A; A/B=1-214.
DR PDBsum; 1G3U; -.
DR PDBsum; 1GSI; -.
DR PDBsum; 1GTV; -.
DR PDBsum; 1MRN; -.
DR PDBsum; 1MRS; -.
DR PDBsum; 1N5I; -.
DR PDBsum; 1N5J; -.
DR PDBsum; 1N5K; -.
DR PDBsum; 1N5L; -.
DR PDBsum; 1W2G; -.
DR PDBsum; 1W2H; -.
DR PDBsum; 4UNN; -.
DR PDBsum; 4UNP; -.
DR PDBsum; 4UNQ; -.
DR PDBsum; 4UNR; -.
DR PDBsum; 4UNS; -.
DR PDBsum; 5NQ5; -.
DR PDBsum; 5NR7; -.
DR PDBsum; 5NRN; -.
DR PDBsum; 5NRQ; -.
DR PDBsum; 6YT1; -.
DR AlphaFoldDB; P9WKE1; -.
DR SMR; P9WKE1; -.
DR STRING; 83332.Rv3247c; -.
DR BindingDB; P9WKE1; -.
DR ChEMBL; CHEMBL2361; -.
DR DrugBank; DB03846; 2'-deoxy-5-(hydroxymethyl)uridine 5'-(dihydrogen phosphate).
DR DrugBank; DB03280; p1-(5'-adenosyl)p5-(5'-thymidyl)pentaphosphate.
DR DrugBank; DB04485; Thymidine.
DR DrugBank; DB02452; Thymidine 5'-triphosphate.
DR DrugBank; DB01643; Thymidine monophosphate.
DR DrugBank; DB03666; Zidovudine monophosphate.
DR DrugCentral; P9WKE1; -.
DR PaxDb; P9WKE1; -.
DR DNASU; 888740; -.
DR GeneID; 888740; -.
DR KEGG; mtu:Rv3247c; -.
DR TubercuList; Rv3247c; -.
DR eggNOG; COG0125; Bacteria.
DR OMA; FPRYGRS; -.
DR PhylomeDB; P9WKE1; -.
DR BioCyc; MetaCyc:G185E-7521-MON; -.
DR BRENDA; 2.7.4.9; 3445.
DR SABIO-RK; P9WKE1; -.
DR UniPathway; UPA00575; -.
DR PRO; PR:P9WKE1; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IDA:MTBBASE.
DR GO; GO:0005525; F:GTP binding; IDA:MTBBASE.
DR GO; GO:0000287; F:magnesium ion binding; IDA:MTBBASE.
DR GO; GO:0042803; F:protein homodimerization activity; IPI:MTBBASE.
DR GO; GO:0004798; F:thymidylate kinase activity; IDA:MTBBASE.
DR GO; GO:0009041; F:uridylate kinase activity; IBA:GO_Central.
DR GO; GO:0006233; P:dTDP biosynthetic process; IBA:GO_Central.
DR GO; GO:0006235; P:dTTP biosynthetic process; IBA:GO_Central.
DR GO; GO:0006227; P:dUDP biosynthetic process; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0046044; P:TMP metabolic process; IDA:MTBBASE.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_00165; Thymidylate_kinase; 1.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR039430; Thymidylate_kin-like_dom.
DR InterPro; IPR018095; Thymidylate_kin_CS.
DR InterPro; IPR018094; Thymidylate_kinase.
DR Pfam; PF02223; Thymidylate_kin; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS01331; THYMIDYLATE_KINASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Direct protein sequencing; Kinase; Magnesium;
KW Metal-binding; Nucleotide biosynthesis; Nucleotide-binding;
KW Reference proteome; Transferase.
FT CHAIN 1..214
FT /note="Thymidylate kinase"
FT /id="PRO_0000155309"
FT REGION 147..159
FT /note="LID"
FT BINDING 7..14
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 9
FT /ligand="dTMP"
FT /ligand_id="ChEBI:CHEBI:63528"
FT BINDING 9
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 39
FT /ligand="dTMP"
FT /ligand_id="ChEBI:CHEBI:63528"
FT BINDING 70
FT /ligand="dTMP"
FT /ligand_id="ChEBI:CHEBI:63528"
FT BINDING 74
FT /ligand="dTMP"
FT /ligand_id="ChEBI:CHEBI:63528"
FT BINDING 95
FT /ligand="dTMP"
FT /ligand_id="ChEBI:CHEBI:63528"
FT BINDING 100
FT /ligand="dTMP"
FT /ligand_id="ChEBI:CHEBI:63528"
FT BINDING 103
FT /ligand="dTMP"
FT /ligand_id="ChEBI:CHEBI:63528"
FT BINDING 163
FT /ligand="dTMP"
FT /ligand_id="ChEBI:CHEBI:63528"
FT BINDING 165
FT /ligand="dTMP"
FT /ligand_id="ChEBI:CHEBI:63528"
FT BINDING 166
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT SITE 153
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255"
FT STRAND 2..12
FT /evidence="ECO:0007829|PDB:1GTV"
FT HELIX 13..25
FT /evidence="ECO:0007829|PDB:1GTV"
FT STRAND 26..47
FT /evidence="ECO:0007829|PDB:1GTV"
FT HELIX 48..51
FT /evidence="ECO:0007829|PDB:1GTV"
FT STRAND 52..62
FT /evidence="ECO:0007829|PDB:1GTV"
FT HELIX 63..74
FT /evidence="ECO:0007829|PDB:1GTV"
FT STRAND 75..79
FT /evidence="ECO:0007829|PDB:1GTV"
FT HELIX 80..83
FT /evidence="ECO:0007829|PDB:1GTV"
FT STRAND 84..97
FT /evidence="ECO:0007829|PDB:1GTV"
FT HELIX 98..107
FT /evidence="ECO:0007829|PDB:1GTV"
FT STRAND 108..114
FT /evidence="ECO:0007829|PDB:1GTV"
FT HELIX 115..123
FT /evidence="ECO:0007829|PDB:1GTV"
FT STRAND 124..129
FT /evidence="ECO:0007829|PDB:1GTV"
FT STRAND 134..142
FT /evidence="ECO:0007829|PDB:1GTV"
FT HELIX 143..155
FT /evidence="ECO:0007829|PDB:1GTV"
FT STRAND 158..168
FT /evidence="ECO:0007829|PDB:1GTV"
FT HELIX 169..183
FT /evidence="ECO:0007829|PDB:1GTV"
FT STRAND 184..198
FT /evidence="ECO:0007829|PDB:1GTV"
FT HELIX 200..207
FT /evidence="ECO:0007829|PDB:1GTV"
SQ SEQUENCE 214 AA; 22635 MW; E435123C250F46E7 CRC64;
MLIAIEGVDG AGKRTLVEKL SGAFRAAGRS VATLAFPRYG QSVAADIAAE ALHGEHGDLA
SSVYAMATLF ALDRAGAVHT IQGLCRGYDV VILDRYVASN AAYSAARLHE NAAGKAAAWV
QRIEFARLGL PKPDWQVLLA VSAELAGERS RGRAQRDPGR ARDNYERDAE LQQRTGAVYA
ELAAQGWGGR WLVVGADVDP GRLAATLAPP DVPS
