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KCY1_ORYSJ
ID   KCY1_ORYSJ              Reviewed;         243 AA.
AC   Q5VRN0; A0A0P0WRX7;
DT   03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT   07-DEC-2004, sequence version 1.
DT   03-AUG-2022, entry version 130.
DE   RecName: Full=UMP-CMP kinase 1 {ECO:0000255|HAMAP-Rule:MF_03172};
DE            EC=2.7.4.14 {ECO:0000255|HAMAP-Rule:MF_03172};
DE   AltName: Full=Deoxycytidylate kinase 1 {ECO:0000255|HAMAP-Rule:MF_03172};
DE            Short=CK 1 {ECO:0000255|HAMAP-Rule:MF_03172};
DE            Short=dCMP kinase 1 {ECO:0000255|HAMAP-Rule:MF_03172};
DE   AltName: Full=Uridine monophosphate/cytidine monophosphate kinase 1 {ECO:0000255|HAMAP-Rule:MF_03172};
DE            Short=UMP/CMP kinase 1 {ECO:0000255|HAMAP-Rule:MF_03172};
DE            Short=UMP/CMPK 1 {ECO:0000255|HAMAP-Rule:MF_03172};
GN   OrderedLocusNames=Os06g0109600, LOC_Os06g02000;
GN   ORFNames=OsJ_19856, OSJNBa0004I20.14, P0514G12.38;
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=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   [2]
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   [3]
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   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
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}.
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DR   EMBL; AP000616; BAD67693.1; -; Genomic_DNA.
DR   EMBL; AP002805; BAD67896.1; -; Genomic_DNA.
DR   EMBL; AP008212; BAF18492.1; -; Genomic_DNA.
DR   EMBL; AP014962; BAS95779.1; -; Genomic_DNA.
DR   EMBL; CM000143; EEE64963.1; -; Genomic_DNA.
DR   EMBL; AK066989; BAG90214.1; -; mRNA.
DR   RefSeq; XP_015641837.1; XM_015786351.1.
DR   RefSeq; XP_015641838.1; XM_015786352.1.
DR   AlphaFoldDB; Q5VRN0; -.
DR   SMR; Q5VRN0; -.
DR   STRING; 4530.OS06T0109600-01; -.
DR   PaxDb; Q5VRN0; -.
DR   PRIDE; Q5VRN0; -.
DR   EnsemblPlants; Os06t0109600-01; Os06t0109600-01; Os06g0109600.
DR   GeneID; 4339882; -.
DR   Gramene; Os06t0109600-01; Os06t0109600-01; Os06g0109600.
DR   KEGG; osa:4339882; -.
DR   eggNOG; KOG3079; Eukaryota.
DR   HOGENOM; CLU_032354_0_1_1; -.
DR   InParanoid; Q5VRN0; -.
DR   OMA; TKMEPEF; -.
DR   OrthoDB; 1378291at2759; -.
DR   Proteomes; UP000000763; Chromosome 6.
DR   Proteomes; UP000007752; Chromosome 6.
DR   Proteomes; UP000059680; Chromosome 6.
DR   Genevisible; Q5VRN0; 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..243
FT                   /note="UMP-CMP kinase 1"
FT                   /id="PRO_0000430121"
FT   REGION          49..78
FT                   /note="NMP"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT   REGION          141..149
FT                   /note="LID"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT   BINDING         29..34
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT   BINDING         55
FT                   /ligand="a ribonucleoside 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:58043"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT   BINDING         76..78
FT                   /ligand="a ribonucleoside 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:58043"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT   BINDING         103..106
FT                   /ligand="a ribonucleoside 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:58043"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT   BINDING         110
FT                   /ligand="CMP"
FT                   /ligand_id="ChEBI:CHEBI:60377"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT   BINDING         142
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT   BINDING         146
FT                   /ligand="a ribonucleoside 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:58043"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT   BINDING         157
FT                   /ligand="a ribonucleoside 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:58043"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT   BINDING         185
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
SQ   SEQUENCE   243 AA;  27947 MW;  94C220053A7B664A CRC64;
     MAHANKNHIE SFPPPGKKIT IVFVIGGPGS GKGTQCAKIV KQFGFTHLSA GDLLREEAKY
     DTEQGTMIKN LMNEGKLVSS DLIVKLLFKA MRESGNDKFL VDGFPRNEEN RHAYENIIHI
     EPEFLLFIDC SKEEMERRIL NRNQGRDDDN IDTIRRRFDV FQQQTLPVIQ YYEKRGKLRK
     VDGNRQVDEV FEDVKAIFAQ LNNQKIHGGQ QASGLSRAQM NPLKRWFFDF FCGCFGTKEE
     ARN
 
 
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