KTHY_YEAST
ID KTHY_YEAST Reviewed; 216 AA.
AC P00572; D6VWM8;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 2.
DT 03-AUG-2022, entry version 188.
DE RecName: Full=Thymidylate kinase;
DE EC=2.7.4.9 {ECO:0000269|PubMed:6088527};
DE AltName: Full=dTMP kinase;
GN Name=CDC8; OrderedLocusNames=YJR057W; ORFNames=J1715;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-22, FUNCTION, AND
RP CATALYTIC ACTIVITY.
RX PubMed=6088527; DOI=10.1016/s0021-9258(18)90621-6;
RA Jong A.Y.S., Kuo C.-L., Campbell J.L.;
RT "The CDC8 gene of yeast encodes thymidylate kinase.";
RL J. Biol. Chem. 259:11052-11059(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6371491; DOI=10.1128/mcb.4.4.583-590.1984;
RA Birkenmeyer L.G., Hill J.C., Dumas L.B.;
RT "Saccharomyces cerevisiae CDC8 gene and its product.";
RL Mol. Cell. Biol. 4:583-590(1984).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8840504;
RX DOI=10.1002/(sici)1097-0061(199607)12:9<869::aid-yea964>3.0.co;2-1;
RA Huang M.-E., Manus V., Chuat J.-C., Galibert F.;
RT "Analysis of a 62 kb DNA sequence of chromosome X reveals 36 open reading
RT frames and a gene cluster with a counterpart on chromosome XI.";
RL Yeast 12:869-875(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL EMBO J. 15:2031-2049(1996).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
RX PubMed=9253404; DOI=10.1038/nsb0897-601;
RA Lavie A., Vetter I.R., Konrad M., Goody R.S., Reinstein J., Schlichting I.;
RT "Structure of thymidylate kinase reveals the cause behind the limiting step
RT in AZT activation.";
RL Nat. Struct. Biol. 4:601-604(1997).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX PubMed=9521686; DOI=10.1021/bi9720787;
RA Lavie A., Konrad M., Brundiers R., Goody R.S., Schlichting I.,
RA Reinstein J.;
RT "Crystal structure of yeast thymidylate kinase complexed with the
RT bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-thymidyl) pentaphosphate
RT (TP5A) at 2.0-A resolution: implications for catalysis and AZT
RT activation.";
RL Biochemistry 37:3677-3686(1998).
CC -!- FUNCTION: Catalyzes the conversion of dTMP to dTDP.
CC {ECO:0000269|PubMed:6088527}.
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:6088527};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13518;
CC Evidence={ECO:0000269|PubMed:6088527};
CC -!- PATHWAY: Pyrimidine metabolism; dTTP biosynthesis.
CC {ECO:0000305|PubMed:6088527}.
CC -!- SUBUNIT: Homodimer.
CC -!- INTERACTION:
CC P00572; P47035: NET1; NbExp=2; IntAct=EBI-9957, EBI-25953;
CC -!- MISCELLANEOUS: Present with 2980 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the thymidylate kinase family. {ECO:0000305}.
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DR EMBL; K02116; AAA35158.1; -; Genomic_DNA.
DR EMBL; K01783; AAA34486.1; -; Genomic_DNA.
DR EMBL; Z49557; CAA89585.1; -; Genomic_DNA.
DR EMBL; M15468; AAB05644.1; -; Genomic_DNA.
DR EMBL; L47993; AAB39283.1; -; Genomic_DNA.
DR EMBL; BK006943; DAA08844.1; -; Genomic_DNA.
DR PIR; S57076; KIBYT8.
DR RefSeq; NP_012591.1; NM_001181715.1.
DR PDB; 1TMK; X-ray; 2.10 A; A/B=1-216.
DR PDB; 2TMK; X-ray; 2.40 A; A/B=1-216.
DR PDB; 3TMK; X-ray; 2.00 A; A/B/C/D/E/F/G/H=1-216.
DR PDBsum; 1TMK; -.
DR PDBsum; 2TMK; -.
DR PDBsum; 3TMK; -.
DR AlphaFoldDB; P00572; -.
DR SMR; P00572; -.
DR BioGRID; 33814; 675.
DR IntAct; P00572; 5.
DR MINT; P00572; -.
DR STRING; 4932.YJR057W; -.
DR MaxQB; P00572; -.
DR PaxDb; P00572; -.
DR PRIDE; P00572; -.
DR EnsemblFungi; YJR057W_mRNA; YJR057W; YJR057W.
DR GeneID; 853520; -.
DR KEGG; sce:YJR057W; -.
DR SGD; S000003818; CDC8.
DR VEuPathDB; FungiDB:YJR057W; -.
DR eggNOG; KOG3327; Eukaryota.
DR GeneTree; ENSGT00940000154030; -.
DR HOGENOM; CLU_049131_3_2_1; -.
DR InParanoid; P00572; -.
DR OMA; MCLFLRI; -.
DR BioCyc; MetaCyc:YJR057W-MON; -.
DR BioCyc; YEAST:YJR057W-MON; -.
DR UniPathway; UPA00575; -.
DR EvolutionaryTrace; P00572; -.
DR PRO; PR:P00572; -.
DR Proteomes; UP000002311; Chromosome X.
DR RNAct; P00572; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IDA:SGD.
DR GO; GO:0004798; F:thymidylate kinase activity; IDA:SGD.
DR GO; GO:0009041; F:uridylate kinase activity; IDA:SGD.
DR GO; GO:0006233; P:dTDP biosynthetic process; IDA:SGD.
DR GO; GO:0006235; P:dTTP biosynthetic process; IDA:SGD.
DR GO; GO:0006227; P:dUDP biosynthetic process; IDA:SGD.
DR GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IDA:SGD.
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 TIGRFAMs; TIGR00041; DTMP_kinase; 1.
DR PROSITE; PS01331; THYMIDYLATE_KINASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Direct protein sequencing; Kinase;
KW Nucleotide biosynthesis; Nucleotide-binding; Reference proteome;
KW Transferase.
FT CHAIN 1..216
FT /note="Thymidylate kinase"
FT /id="PRO_0000155214"
FT BINDING 12..19
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305"
FT CONFLICT 57
FT /note="S -> T (in Ref. 2; AAA34486)"
FT /evidence="ECO:0000305"
FT CONFLICT 188
FT /note="G -> D (in Ref. 1; AAA35158)"
FT /evidence="ECO:0000305"
FT STRAND 7..12
FT /evidence="ECO:0007829|PDB:3TMK"
FT STRAND 14..17
FT /evidence="ECO:0007829|PDB:3TMK"
FT HELIX 18..29
FT /evidence="ECO:0007829|PDB:3TMK"
FT STRAND 31..39
FT /evidence="ECO:0007829|PDB:3TMK"
FT HELIX 44..54
FT /evidence="ECO:0007829|PDB:3TMK"
FT HELIX 62..74
FT /evidence="ECO:0007829|PDB:3TMK"
FT HELIX 77..85
FT /evidence="ECO:0007829|PDB:3TMK"
FT STRAND 89..94
FT /evidence="ECO:0007829|PDB:3TMK"
FT HELIX 96..104
FT /evidence="ECO:0007829|PDB:3TMK"
FT HELIX 113..117
FT /evidence="ECO:0007829|PDB:3TMK"
FT HELIX 118..120
FT /evidence="ECO:0007829|PDB:3TMK"
FT STRAND 123..125
FT /evidence="ECO:0007829|PDB:2TMK"
FT STRAND 127..133
FT /evidence="ECO:0007829|PDB:3TMK"
FT HELIX 140..142
FT /evidence="ECO:0007829|PDB:3TMK"
FT STRAND 145..147
FT /evidence="ECO:0007829|PDB:3TMK"
FT HELIX 154..173
FT /evidence="ECO:0007829|PDB:3TMK"
FT STRAND 178..183
FT /evidence="ECO:0007829|PDB:3TMK"
FT HELIX 189..205
FT /evidence="ECO:0007829|PDB:3TMK"
SQ SEQUENCE 216 AA; 24687 MW; F9A1CA0D56DCD1F6 CRC64;
MMGRGKLILI EGLDRTGKTT QCNILYKKLQ PNCKLLKFPE RSTRIGGLIN EYLTDDSFQL
SDQAIHLLFS ANRWEIVDKI KKDLLEGKNI VMDRYVYSGV AYSAAKGTNG MDLDWCLQPD
VGLLKPDLTL FLSTQDVDNN AEKSGFGDER YETVKFQEKV KQTFMKLLDK EIRKGDESIT
IVDVTNKGIQ EVEALIWQIV EPVLSTHIDH DKFSFF
