KCY3_ORYSJ
ID KCY3_ORYSJ Reviewed; 210 AA.
AC Q7XI40; A0A0P0X943; Q9SE47; Q9SE48;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2003, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=UMP-CMP kinase 3 {ECO:0000255|HAMAP-Rule:MF_03172};
DE EC=2.7.4.14 {ECO:0000255|HAMAP-Rule:MF_03172};
DE AltName: Full=Deoxycytidylate kinase 3 {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=CK 3 {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=dCMP kinase 3 {ECO:0000255|HAMAP-Rule:MF_03172};
DE AltName: Full=UMP/CMP kinase a;
DE AltName: Full=UMP/CMP kinase b;
DE AltName: Full=Uridine monophosphate/cytidine monophosphate kinase 3 {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=UMP/CMP kinase 3 {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=UMP/CMPK 3 {ECO:0000255|HAMAP-Rule:MF_03172};
GN Name=URA6; OrderedLocusNames=Os07g0624700, LOC_Os07g43170;
GN ORFNames=P0524E08.133;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Nipponbare;
RA Park S., Thornburg R.W.;
RT "Characterization of UMP kinase cDNAs from rice (Accession Nos. AF187062
RT and AF187063) (PGR 99-174).";
RL Plant Physiol. 121:1383-1383(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
CC -!- FUNCTION: Catalyzes the phosphorylation of pyrimidine nucleoside
CC monophosphates at the expense of ATP. Plays an important role in de
CC novo pyrimidine nucleotide biosynthesis. Has preference for UMP and CMP
CC as phosphate acceptors. {ECO:0000255|HAMAP-Rule:MF_03172}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + UMP = ADP + UDP; Xref=Rhea:RHEA:24400,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:57865, ChEBI:CHEBI:58223,
CC ChEBI:CHEBI:456216; EC=2.7.4.14; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03172};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + CMP = ADP + CDP; Xref=Rhea:RHEA:11600,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:58069, ChEBI:CHEBI:60377,
CC ChEBI:CHEBI:456216; EC=2.7.4.14; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03172};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + dCMP = ADP + dCDP; Xref=Rhea:RHEA:25094,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:57566, ChEBI:CHEBI:58593,
CC ChEBI:CHEBI:456216; EC=2.7.4.14; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03172};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03172};
CC Note=Binds 1 Mg(2+) ion per monomer. {ECO:0000255|HAMAP-Rule:MF_03172};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_03172}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_03172}.
CC Nucleus {ECO:0000255|HAMAP-Rule:MF_03172}.
CC -!- DOMAIN: Consists of three domains, a large central CORE domain and two
CC small peripheral domains, NMPbind and LID, which undergo movements
CC during catalysis. The LID domain closes over the site of phosphoryl
CC transfer upon ATP binding. Assembling and dissambling the active center
CC during each catalytic cycle provides an effective means to prevent ATP
CC hydrolysis. {ECO:0000255|HAMAP-Rule:MF_03172}.
CC -!- SIMILARITY: Belongs to the adenylate kinase family. UMP-CMP kinase
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_03172}.
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DR EMBL; AF187062; AAF23371.1; -; mRNA.
DR EMBL; AF187063; AAF23372.1; -; mRNA.
DR EMBL; AP004341; BAC79912.1; -; Genomic_DNA.
DR EMBL; AP008213; BAF22241.1; -; Genomic_DNA.
DR EMBL; AP014963; BAT02721.1; -; Genomic_DNA.
DR RefSeq; XP_015644853.1; XM_015789367.1.
DR AlphaFoldDB; Q7XI40; -.
DR SMR; Q7XI40; -.
DR STRING; 4530.OS07T0624700-01; -.
DR PRIDE; Q7XI40; -.
DR EnsemblPlants; Os07t0624700-01; Os07t0624700-01; Os07g0624700.
DR GeneID; 4343960; -.
DR Gramene; Os07t0624700-01; Os07t0624700-01; Os07g0624700.
DR KEGG; osa:4343960; -.
DR eggNOG; KOG3079; Eukaryota.
DR HOGENOM; CLU_032354_0_1_1; -.
DR InParanoid; Q7XI40; -.
DR OMA; RFQFTHL; -.
DR OrthoDB; 1378291at2759; -.
DR Proteomes; UP000000763; Chromosome 7.
DR Proteomes; UP000059680; Chromosome 7.
DR Genevisible; Q7XI40; OS.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0036430; F:CMP kinase activity; IEA:RHEA.
DR GO; GO:0004127; F:cytidylate kinase activity; IBA:GO_Central.
DR GO; GO:0036431; F:dCMP kinase activity; IEA:RHEA.
DR GO; GO:0033862; F:UMP kinase activity; IBA:GO_Central.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IEA:InterPro.
DR GO; GO:0046705; P:CDP biosynthetic process; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0006225; P:UDP biosynthetic process; IBA:GO_Central.
DR CDD; cd01428; ADK; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_00235; Adenylate_kinase_Adk; 1.
DR HAMAP; MF_03172; Adenylate_kinase_UMP_CMP_kin; 1.
DR InterPro; IPR000850; Adenylat/UMP-CMP_kin.
DR InterPro; IPR033690; Adenylat_kinase_CS.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR006266; UMP_CMP_kinase.
DR PANTHER; PTHR23359; PTHR23359; 1.
DR PRINTS; PR00094; ADENYLTKNASE.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR01359; UMP_CMP_kin_fam; 1.
DR PROSITE; PS00113; ADENYLATE_KINASE; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; Cytoplasm; Kinase; Nucleotide-binding; Nucleus;
KW Pyrimidine biosynthesis; Reference proteome; Transferase.
FT CHAIN 1..210
FT /note="UMP-CMP kinase 3"
FT /id="PRO_0000430123"
FT REGION 54..83
FT /note="NMP"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT REGION 146..154
FT /note="LID"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 34..39
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 60
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 81..83
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 108..111
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 115
FT /ligand="CMP"
FT /ligand_id="ChEBI:CHEBI:60377"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 147
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 151
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 162
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 190
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT CONFLICT 191
FT /note="P -> S (in Ref. 1; AAF23372)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 210 AA; 23235 MW; AF2745CDEF941A80 CRC64;
MGSVVDAPVV VEGVAENMLG DKKVTVVFVL GGPGSGKGTQ CANIVEHFGF THLSAGDLLR
AEIKSGSENG TMIENMIKEG KIVPSEVTIK LLQDAMIKNE NDKFLIDGFP RNEENRAAFE
NVTKISPAFV LFFDCSEEEM ERRLLGRNQG RVDDNIETIR KRFKVFVESS LPVIEHYNAK
NKVKKIDAAK PISEVFEDVK AIFAPYAKVE
