NDK4_ARATH
ID NDK4_ARATH Reviewed; 237 AA.
AC Q8LAH8; Q9T0A5;
DT 15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2004, sequence version 2.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=Nucleoside diphosphate kinase IV, chloroplastic/mitochondrial;
DE Short=NDK IV;
DE Short=NDP kinase IV;
DE Short=NDPK IV;
DE EC=2.7.4.6;
DE AltName: Full=Nucleoside diphosphate kinase 4;
DE Flags: Precursor;
GN Name=NDK4; OrderedLocusNames=At4g23900; ORFNames=T32A16.70;
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 [GENOMIC DNA].
RC STRAIN=cv. Columbia;
RA Yabe N., Hashimoto K., Hasunuma K.;
RT "Arabidopsis NDP kinase gene NDK4.";
RL Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
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 [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].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP PROTEIN SEQUENCE OF 85-102, 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 {ECO:0000250}. Mitochondrion intermembrane space {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
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DR EMBL; AL078468; CAB43890.1; -; Genomic_DNA.
DR EMBL; AL161560; CAB81308.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84824.1; -; Genomic_DNA.
DR EMBL; AB044970; BAB19789.1; -; Genomic_DNA.
DR EMBL; AK117895; BAC42534.1; -; mRNA.
DR EMBL; AY087800; AAM65336.1; -; mRNA.
DR PIR; T08909; T08909.
DR RefSeq; NP_567690.1; NM_118522.3.
DR AlphaFoldDB; Q8LAH8; -.
DR SMR; Q8LAH8; -.
DR STRING; 3702.AT4G23900.1; -.
DR iPTMnet; Q8LAH8; -.
DR PaxDb; Q8LAH8; -.
DR PRIDE; Q8LAH8; -.
DR ProteomicsDB; 251100; -.
DR EnsemblPlants; AT4G23900.1; AT4G23900.1; AT4G23900.
DR GeneID; 828490; -.
DR Gramene; AT4G23900.1; AT4G23900.1; AT4G23900.
DR KEGG; ath:AT4G23900; -.
DR Araport; AT4G23900; -.
DR TAIR; locus:2138101; AT4G23900.
DR eggNOG; KOG0888; Eukaryota.
DR HOGENOM; CLU_060216_5_0_1; -.
DR InParanoid; Q8LAH8; -.
DR OMA; EEFVNWT; -.
DR OrthoDB; 1334716at2759; -.
DR PhylomeDB; Q8LAH8; -.
DR BioCyc; ARA:AT4G23900-MON; -.
DR PRO; PR:Q8LAH8; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8LAH8; baseline and differential.
DR Genevisible; Q8LAH8; AT.
DR GO; GO:0009543; C:chloroplast thylakoid lumen; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IEA:UniProtKB-SubCell.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
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..84
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000250"
FT CHAIN 85..237
FT /note="Nucleoside diphosphate kinase IV,
FT chloroplastic/mitochondrial"
FT /id="PRO_0000019436"
FT ACT_SITE 201
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 95
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 143
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 171
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 177
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 188
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 198
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT CONFLICT 36
FT /note="S -> T (in Ref. 5; AAM65336)"
FT /evidence="ECO:0000305"
FT CONFLICT 66
FT /note="G -> R (in Ref. 5; AAM65336)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 237 AA; 25773 MW; 0CC2B487E3D376FA CRC64;
MSSQICRSAS RAARSLLSSA KNARFFSEGR AIGAASVVHA TGKVPQYASN FGKSGSGFVS
NSWITGLLAL PAAAFMLQDQ EALAAEMERT FIAIKPDGVQ RGLISEIITR FERKGYKLVG
IKVMVPSKGF AQKHYHDLKE RPFFNGLCNF LSSGPVVAMV WEGEGVIRYG RKLIGATDPQ
KSEPGTIRGD LAVVVGRNII HGSDGPETAK DEISLWFKPE ELVSYTSNAE KWIYGQN
