KCY3_ARATH
ID KCY3_ARATH Reviewed; 202 AA.
AC O04905; A0JQ75;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 03-AUG-2022, entry version 139.
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 {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=CK {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=dCMP kinase {ECO:0000255|HAMAP-Rule:MF_03172};
DE AltName: Full=Uridine monophosphate/cytidine monophosphate kinase {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=UMP/CMP kinase {ECO:0000255|HAMAP-Rule:MF_03172};
DE Short=UMP/CMPK {ECO:0000255|HAMAP-Rule:MF_03172};
GN Name=UMK3; Synonyms=PYR6; OrderedLocusNames=At5g26667; ORFNames=T7I7.5;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 1-15, CATALYTIC
RP ACTIVITY, MASS SPECTROMETRY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, AND REACTION MECHANISM.
RX PubMed=9576794; DOI=10.1104/pp.117.1.245;
RA Zhou L., Lacroute F., Thornburg R.;
RT "Cloning, expression in Escherichia coli, and characterization of
RT Arabidopsis thaliana UMP/CMP kinase.";
RL Plant Physiol. 117:245-254(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RA Bautista V.R., Kim C.J., Chen H., Quinitio C., Ecker J.R.;
RT "Arabidopsis ORF Clones.";
RL Submitted (NOV-2006) to the EMBL/GenBank/DDBJ databases.
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. Does not act on dCMP and dUMP.
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, ECO:0000269|PubMed:9576794};
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, ECO:0000269|PubMed:9576794};
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, ECO:0000269|PubMed:9576794};
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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=29.3 uM for ATP (with UMP as cosubstrate)
CC {ECO:0000269|PubMed:9576794};
CC KM=291.7 uM for ATP (with CMP as cosubstrate)
CC {ECO:0000269|PubMed:9576794};
CC KM=152.9 uM for UMP {ECO:0000269|PubMed:9576794};
CC KM=266.4 uM for CMP {ECO:0000269|PubMed:9576794};
CC pH dependence:
CC Optimum pH is 6.5. {ECO:0000269|PubMed:9576794};
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=O04905-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O04905-2; Sequence=VSP_053919;
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 -!- MASS SPECTROMETRY: Mass=22405; Mass_error=185; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:9576794};
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; AF000147; AAB71135.1; -; mRNA.
DR EMBL; AC137518; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED93558.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93559.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93560.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM70813.1; -; Genomic_DNA.
DR EMBL; BT029445; ABK59674.1; -; mRNA.
DR RefSeq; NP_001031942.1; NM_001036865.1. [O04905-1]
DR RefSeq; NP_001332394.1; NM_001343973.1. [O04905-1]
DR RefSeq; NP_850867.1; NM_180536.3. [O04905-2]
DR RefSeq; NP_850868.1; NM_180537.3. [O04905-1]
DR AlphaFoldDB; O04905; -.
DR SMR; O04905; -.
DR BioGRID; 17985; 3.
DR IntAct; O04905; 3.
DR STRING; 3702.AT5G26667.1; -.
DR iPTMnet; O04905; -.
DR PaxDb; O04905; -.
DR PRIDE; O04905; -.
DR ProteomicsDB; 247323; -. [O04905-1]
DR EnsemblPlants; AT5G26667.1; AT5G26667.1; AT5G26667. [O04905-2]
DR EnsemblPlants; AT5G26667.2; AT5G26667.2; AT5G26667. [O04905-1]
DR EnsemblPlants; AT5G26667.3; AT5G26667.3; AT5G26667. [O04905-1]
DR EnsemblPlants; AT5G26667.4; AT5G26667.4; AT5G26667. [O04905-1]
DR GeneID; 832710; -.
DR Gramene; AT5G26667.1; AT5G26667.1; AT5G26667. [O04905-2]
DR Gramene; AT5G26667.2; AT5G26667.2; AT5G26667. [O04905-1]
DR Gramene; AT5G26667.3; AT5G26667.3; AT5G26667. [O04905-1]
DR Gramene; AT5G26667.4; AT5G26667.4; AT5G26667. [O04905-1]
DR KEGG; ath:AT5G26667; -.
DR Araport; AT5G26667; -.
DR TAIR; locus:1005716878; AT5G26667.
DR eggNOG; KOG3079; Eukaryota.
DR HOGENOM; CLU_032354_0_1_1; -.
DR InParanoid; O04905; -.
DR OMA; RFQFTHL; -.
DR PhylomeDB; O04905; -.
DR BioCyc; ARA:AT5G26667-MON; -.
DR BioCyc; MetaCyc:AT5G26667-MON; -.
DR BRENDA; 2.7.4.14; 399.
DR PRO; PR:O04905; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; O04905; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IDA:UniProtKB.
DR GO; GO:0036430; F:CMP kinase activity; IEA:RHEA.
DR GO; GO:0004127; F:cytidylate kinase activity; IDA:UniProtKB.
DR GO; GO:0036431; F:dCMP kinase activity; IEA:RHEA.
DR GO; GO:0033862; F:UMP kinase activity; IBA:GO_Central.
DR GO; GO:0009041; F:uridylate kinase activity; IDA:TAIR.
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:0006221; P:pyrimidine nucleotide biosynthetic process; IDA:UniProtKB.
DR GO; GO:0009173; P:pyrimidine ribonucleoside monophosphate metabolic process; TAS:TAIR.
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 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Cytoplasm; Direct protein sequencing;
KW Kinase; Nucleotide-binding; Nucleus; Pyrimidine biosynthesis;
KW Reference proteome; Transferase.
FT CHAIN 1..202
FT /note="UMP-CMP kinase 3"
FT /id="PRO_0000158945"
FT REGION 44..73
FT /note="NMP"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT REGION 136..144
FT /note="LID"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 24..29
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 50
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 71..73
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 98..101
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 105
FT /ligand="CMP"
FT /ligand_id="ChEBI:CHEBI:60377"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 137
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 141
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 152
FT /ligand="a ribonucleoside 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:58043"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT BINDING 180
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03172"
FT VAR_SEQ 201..202
FT /note="EA -> KLNSCAIL (in isoform 2)"
FT /evidence="ECO:0000303|Ref.4"
FT /id="VSP_053919"
SQ SEQUENCE 202 AA; 22482 MW; 41AD0CFACD816315 CRC64;
MGSVDAANGS GKKPTVIFVL GGPGSGKGTQ CAYIVEHYGY THLSAGDLLR AEIKSGSENG
TMIQNMIKEG KIVPSEVTIK LLQKAIQENG NDKFLIDGFP RNEENRAAFE KVTEIEPKFV
LFFDCPEEEM EKRLLGRNQG REDDNIETIR KRFKVFLESS LPVIHYYEAK GKVRKINAAK
PIEAVFEEVK AIFSPEAEKV EA
