KCY2_ORYSJ
ID KCY2_ORYSJ Reviewed; 243 AA.
AC Q7XMI0; Q0JFG3;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 03-SEP-2014, sequence version 3.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=UMP-CMP kinase 2 {ECO:0000255|HAMAP-Rule:MF_03172};
DE EC=2.7.4.14 {ECO:0000255|HAMAP-Rule:MF_03172};
DE AltName: Full=Deoxycytidylate kinase 2 {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=CK 2 {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=dCMP kinase 2 {ECO:0000255|HAMAP-Rule:MF_03172};
DE AltName: Full=Uridine monophosphate/cytidine monophosphate kinase 2 {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=UMP/CMP kinase 2 {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=UMP/CMPK 2 {ECO:0000255|HAMAP-Rule:MF_03172};
GN OrderedLocusNames=Os04g0105500, LOC_Os04g01530; ORFNames=OSJNBb0004G23.5;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447439; DOI=10.1038/nature01183;
RA Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y.,
RA Hu X., Jia P., Zhang Y., Zhao Q., Ying K., Yu S., Tang Y., Weng Q.,
RA Zhang L., Lu Y., Mu J., Lu Y., Zhang L.S., Yu Z., Fan D., Liu X., Lu T.,
RA Li C., Wu Y., Sun T., Lei H., Li T., Hu H., Guan J., Wu M., Zhang R.,
RA Zhou B., Chen Z., Chen L., Jin Z., Wang R., Yin H., Cai Z., Ren S., Lv G.,
RA Gu W., Zhu G., Tu Y., Jia J., Zhang Y., Chen J., Kang H., Chen X., Shao C.,
RA Sun Y., Hu Q., Zhang X., Zhang W., Wang L., Ding C., Sheng H., Gu J.,
RA Chen S., Ni L., Zhu F., Chen W., Lan L., Lai Y., Cheng Z., Gu M., Jiang J.,
RA Li J., Hong G., Xue Y., Han B.;
RT "Sequence and analysis of rice chromosome 4.";
RL Nature 420:316-320(2002).
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).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF13924.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAE04607.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL662992; CAE04607.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008210; BAF13924.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014960; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AK071444; -; NOT_ANNOTATED_CDS; mRNA.
DR AlphaFoldDB; Q7XMI0; -.
DR SMR; Q7XMI0; -.
DR STRING; 4530.OS04T0105500-02; -.
DR PaxDb; Q7XMI0; -.
DR PRIDE; Q7XMI0; -.
DR eggNOG; KOG3079; Eukaryota.
DR HOGENOM; CLU_032354_0_1_1; -.
DR InParanoid; Q7XMI0; -.
DR Proteomes; UP000000763; Chromosome 4.
DR Proteomes; UP000059680; Chromosome 4.
DR Genevisible; Q7XMI0; OS.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005759; C:mitochondrial matrix; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0004017; F:adenylate kinase activity; 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:0036431; F:dCMP kinase activity; IEA:RHEA.
DR GO; GO:0046899; F:nucleoside triphosphate adenylate kinase activity; IBA:GO_Central.
DR GO; GO:0033862; F:UMP kinase activity; IEA:RHEA.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IEA:InterPro.
DR GO; GO:0046033; P:AMP metabolic process; IBA:GO_Central.
DR GO; GO:0009142; P:nucleoside triphosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0006221; P:pyrimidine nucleotide biosynthetic process; IEA:UniProtKB-UniRule.
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..243
FT /note="UMP-CMP kinase 2"
FT /id="PRO_0000430122"
FT REGION 89..118
FT /note="NMP"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT REGION 181..189
FT /note="LID"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 69..74
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 95
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 116..118
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 143..146
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 150
FT /ligand="CMP"
FT /ligand_id="ChEBI:CHEBI:60377"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 182
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 186
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 197
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT CONFLICT 33
FT /note="S -> T (in Ref. 1; CAE04607)"
FT /evidence="ECO:0000305"
FT CONFLICT 193
FT /note="T -> A (in Ref. 5; AK071444)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 243 AA; 26967 MW; DA110441772E17A2 CRC64;
MWRRQVGALL LRHRSTPSST LRHHLPLPVP DQSPPLASNL LLRLFTSQSG EGGDGATKPF
IAFVLGGPGS GKGTQCVRIA SDFGFAHLSA GDLLRSEIST GREKGELILN IIKEGKIVPS
EITVELIRKA MESSDAKRVL IDGFPRCEEN RIAFERITGT EPDLVIFFDC PEDEMVKRLL
GRNQGRVDDN IETIKKRLKV FESLNIPVVD YYTSRGKVHK INATGTEEEI FGAVHKLFSS
LRF
