NDK3_ARATH
ID NDK3_ARATH Reviewed; 238 AA.
AC O49203;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=Nucleoside diphosphate kinase III, chloroplastic/mitochondrial;
DE Short=NDK III;
DE Short=NDP kinase III;
DE Short=NDPK III;
DE EC=2.7.4.6;
DE Flags: Precursor;
GN Name=NDPK3; OrderedLocusNames=At4g11010; ORFNames=F25I24.220, F8M12.12;
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], SUBCELLULAR LOCATION, AND CHARACTERIZATION.
RC STRAIN=cv. Columbia;
RX PubMed=14736920; DOI=10.1073/pnas.0308164100;
RA Spetea C., Hundal T., Lundin B., Heddad M., Adamska I., Andersson B.;
RT "Multiple evidence for nucleotide metabolism in the chloroplast thylakoid
RT lumen.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:1409-1414(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Columbia;
RA Lee J., Song P.-S., Hahn T.R., Choi G.;
RL Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP PROTEIN SEQUENCE OF 86-103 AND 122-135, AND SUBCELLULAR LOCATION.
RC TISSUE=Leaf, and Stem;
RX PubMed=11743114; DOI=10.1104/pp.010474;
RA Kruft V., Eubel H., Jaensch L., Werhahn W., Braun H.-P.;
RT "Proteomic approach to identify novel mitochondrial proteins in
RT Arabidopsis.";
RL Plant Physiol. 127:1694-1710(2001).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=14671022; DOI=10.1105/tpc.016055;
RA Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
RA Millar A.H.;
RT "Experimental analysis of the Arabidopsis mitochondrial proteome highlights
RT signaling and regulatory components, provides assessment of targeting
RT prediction programs, and indicates plant-specific mitochondrial proteins.";
RL Plant Cell 16:241-256(2004).
CC -!- FUNCTION: Major role in the synthesis of nucleoside triphosphates other
CC than ATP. The ATP gamma phosphate is transferred to the NDP beta
CC phosphate via a ping-pong mechanism, using a phosphorylated active-site
CC intermediate. Shows the highest specificity towards GDP (By
CC similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-
CC deoxyribonucleoside 5'-triphosphate + ADP; Xref=Rhea:RHEA:44640,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:61560, ChEBI:CHEBI:73316,
CC ChEBI:CHEBI:456216; EC=2.7.4.6;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-
CC triphosphate + ADP; Xref=Rhea:RHEA:18113, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:61557, ChEBI:CHEBI:456216; EC=2.7.4.6;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- SUBUNIT: Homohexamer. {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid lumen.
CC Mitochondrion intermembrane space.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
CC -!- CAUTION: PubMed:14736920 demonstrates a thylakoid lumen location, while
CC PubMed:14671022 shows a mitochondrial location. {ECO:0000305}.
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DR EMBL; AF044265; AAC00512.1; -; mRNA.
DR EMBL; AF080118; AAC33956.1; -; Genomic_DNA.
DR EMBL; AL049525; CAB40069.1; -; Genomic_DNA.
DR EMBL; AL161518; CAB81202.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE82961.1; -; Genomic_DNA.
DR EMBL; AY062964; AAL33810.1; -; mRNA.
DR EMBL; AY035184; AAK59688.1; -; mRNA.
DR PIR; T01877; T01877.
DR RefSeq; NP_192839.1; NM_117171.4.
DR AlphaFoldDB; O49203; -.
DR SMR; O49203; -.
DR BioGRID; 12001; 2.
DR STRING; 3702.AT4G11010.1; -.
DR PaxDb; O49203; -.
DR PRIDE; O49203; -.
DR ProteomicsDB; 251166; -.
DR EnsemblPlants; AT4G11010.1; AT4G11010.1; AT4G11010.
DR GeneID; 826702; -.
DR Gramene; AT4G11010.1; AT4G11010.1; AT4G11010.
DR KEGG; ath:AT4G11010; -.
DR Araport; AT4G11010; -.
DR TAIR; locus:2123421; AT4G11010.
DR eggNOG; KOG0888; Eukaryota.
DR HOGENOM; CLU_060216_5_0_1; -.
DR InParanoid; O49203; -.
DR OMA; WFRAEEL; -.
DR OrthoDB; 1334716at2759; -.
DR PhylomeDB; O49203; -.
DR BioCyc; ARA:AT4G11010-MON; -.
DR BRENDA; 2.7.4.6; 399.
DR PRO; PR:O49203; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; O49203; baseline and differential.
DR Genevisible; O49203; AT.
DR GO; GO:0009543; C:chloroplast thylakoid lumen; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005743; C:mitochondrial inner membrane; IDA:TAIR.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IEA:UniProtKB-SubCell.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0050897; F:cobalt ion binding; HDA:TAIR.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; HDA:TAIR.
DR GO; GO:0006241; P:CTP biosynthetic process; IEA:InterPro.
DR GO; GO:0006183; P:GTP biosynthetic process; IEA:InterPro.
DR GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IEA:InterPro.
DR GO; GO:0006228; P:UTP biosynthetic process; IEA:InterPro.
DR Gene3D; 3.30.70.141; -; 1.
DR HAMAP; MF_00451; NDP_kinase; 1.
DR InterPro; IPR034907; NDK-like_dom.
DR InterPro; IPR036850; NDK-like_dom_sf.
DR InterPro; IPR001564; Nucleoside_diP_kinase.
DR InterPro; IPR023005; Nucleoside_diP_kinase_AS.
DR Pfam; PF00334; NDK; 1.
DR PRINTS; PR01243; NUCDPKINASE.
DR SMART; SM00562; NDK; 1.
DR SUPFAM; SSF54919; SSF54919; 1.
DR PROSITE; PS00469; NDP_KINASES; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Chloroplast; Direct protein sequencing; Kinase; Magnesium;
KW Metal-binding; Mitochondrion; Nucleotide metabolism; Nucleotide-binding;
KW Plastid; Reference proteome; Thylakoid; Transferase; Transit peptide.
FT TRANSIT 1..85
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000269|PubMed:11743114"
FT CHAIN 86..238
FT /note="Nucleoside diphosphate kinase III,
FT chloroplastic/mitochondrial"
FT /id="PRO_0000019435"
FT ACT_SITE 202
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 96
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 144
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 172
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 178
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 189
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 199
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
SQ SEQUENCE 238 AA; 25734 MW; 6F05190005F7A1D9 CRC64;
MSSQICRSAS KAAKSLLSSA KNARFFSEGR AIGAAAAVSA SGKIPLYASN FARSSGSGVA
SKSWITGLLA LPAAAYMIQD QEVLAAEMER TFIAIKPDGV QRGLISEIIS RFERKGFKLV
GIKVIVPSKD FAQKHYHDLK ERPFFNGLCD FLSSGPVIAM VWEGDGVIRY GRKLIGATDP
QKSEPGTIRG DLAVTVGRNI IHGSDGPETA KDEISLWFKP QELVSYTSNS EKWLYGDN
