ID   NDK1_ARATH              Reviewed;         149 AA.
AC   P39207; F4JJZ8; Q41989; Q94JY5;
DT   01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1995, sequence version 1.
DT   02-SEP-2026, entry version 183.
DE   RecName: Full=Nucleoside diphosphate kinase 1;
DE            EC=2.7.4.6;
DE   AltName: Full=Nucleoside diphosphate kinase I;
DE            Short=NDK I;
DE            Short=NDP kinase I;
DE            Short=NDPK I;
GN   Name=NDK1; Synonyms=NDPK1; OrderedLocusNames=At4g09320;
GN   ORFNames=T30A10.80;
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 / MRNA].
RC   STRAIN=cv. C24, and cv. Columbia;
RA   Quigley F.R.;
RL   Submitted (NOV-1992) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   STRAIN=cv. Columbia;
RA   Yi H., Shin B., Lee J., Song P.-S., Choi G.;
RT   "Cloning and characterization of a phytochrome interacting protein.";
RL   Submitted (AUG-1997) 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   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RG   The Arabidopsis Information Resource (TAIR);
RT   "Community-consensus reference genome of Arabidopsis thaliana Col-0.";
RL   Submitted (FEB-2026) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 4-149.
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   [7]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 5-81.
RC   STRAIN=cv. Columbia; TISSUE=Flower;
RX   PubMed=8281187; DOI=10.1046/j.1365-313x.1993.04061051.x;
RA   Hoefte H., Desprez T., Amselem J., Chiapello H., Rouze P., Caboche M.,
RA   Moisan A., Jourjon M.-F., Charpenteau J.-L., Berthomieu P., Guerrier D.,
RA   Giraudat J., Quigley F., Thomas F., Yu D.-Y., Mache R., Raynal M.,
RA   Cooke R., Grellet F., Delseny M., Parmentier Y., de Marcillac G., Gigot C.,
RA   Fleck J., Philipps G., Axelos M., Bardet C., Tremousaygue D., Lescure B.;
RT   "An inventory of 1152 expressed sequence tags obtained by partial
RT   sequencing of cDNAs from Arabidopsis thaliana.";
RL   Plant J. 4:1051-1061(1993).
RN   [8]
RP   FUNCTION, AND INTERACTION WITH CAT1; CAT2 AND CAT3.
RX   PubMed=14581623; DOI=10.1093/pcp/pcg140;
RA   Fukamatsu Y., Yabe N., Hasunuma K.;
RT   "Arabidopsis NDK1 is a component of ROS signaling by interacting with three
RT   catalases.";
RL   Plant Cell Physiol. 44:982-989(2003).
RN   [9]
RP   SUBCELLULAR LOCATION.
RX   PubMed=19329564; DOI=10.1104/pp.109.137703;
RA   Reumann S., Quan S., Aung K., Yang P., Manandhar-Shrestha K., Holbrook D.,
RA   Linka N., Switzenberg R., Wilkerson C.G., Weber A.P., Olsen L.J., Hu J.;
RT   "In-depth proteome analysis of Arabidopsis leaf peroxisomes combined with
RT   in vivo subcellular targeting verification indicates novel metabolic and
RT   regulatory functions of peroxisomes.";
RL   Plant Physiol. 150:125-143(2009).
RN   [10]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA   Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA   Giglione C.;
RT   "Comparative large-scale characterisation of plant vs. mammal proteins
RT   reveals similar and idiosyncratic N-alpha acetylation features.";
RL   Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN   [11]
RP   X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS).
RX   PubMed=15465053; DOI=10.1016/j.jmb.2004.08.054;
RA   Im Y.J., Kim J.I., Shen Y., Na Y., Han Y.J., Kim S.H., Song P.S., Eom S.H.;
RT   "Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-
RT   2 for phytochrome-mediated light signaling.";
RL   J. Mol. Biol. 343:659-670(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. Plays a role in response to reactive oxygen species (ROS)
CC       stress. {ECO:0000269|PubMed:14581623}.
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: Interacts with CAT1, CAT2 and CAT3.
CC       {ECO:0000269|PubMed:14581623}.
CC   -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000269|PubMed:19329564}. Nucleus
CC       {ECO:0000269|PubMed:19329564}. Cytoplasm {ECO:0000269|PubMed:19329564}.
CC   -!- MISCELLANEOUS: Plants over-expressing NDK1 are more tolerant to
CC       paraquat and have increased ability to eliminate exogenous H(2)O(2).
CC       {ECO:0000305|PubMed:14581623}.
CC   -!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAK48956.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC       Sequence=CAA49173.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; X69373; CAA49170.1; -; mRNA.
DR   EMBL; X69376; CAA49173.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AF017641; AAC17844.1; -; mRNA.
DR   EMBL; AL117386; CAB55695.1; -; Genomic_DNA.
DR   EMBL; AL161514; CAB78055.1; -; Genomic_DNA.
DR   EMBL; CP002687; AEE82742.2; -; Genomic_DNA.
DR   EMBL; OZ408686; CAO7046488.1; -; Genomic_DNA.
DR   EMBL; AF370529; AAK48956.1; ALT_INIT; mRNA.
DR   EMBL; AY072518; AAL66933.1; -; mRNA.
DR   EMBL; Z18791; CAA79265.1; -; mRNA.
DR   PIR; S31444; S31444.
DR   PIR; S31446; S31446.
DR   PIR; T17131; T17131.
DR   RefSeq; NP_567346.2; NM_117000.3.
DR   PDB; 1U8W; X-ray; 2.40 A; A/B/C/D/E/F=1-149.
DR   AlphaFoldDB; P39207; -.
DR   SMR; P39207; -.
DR   BioGRID; 11814; 19.
DR   FunCoup; P39207; 1633.
DR   IntAct; P39207; 4.
DR   STRING; 3702.P39207; -.
DR   iPTMnet; P39207; -.
DR   PaxDb; 3702-P39207; -.
DR   ProMEX; P39207; -.
DR   ProteomicsDB; 251129; -.
DR   GeneID; 826515; -.
DR   KEGG; ath:AT4G09320; -.
DR   Araport; AT4G09320; -.
DR   TAIR; AT4G09320; NDPK1.
DR   eggNOG; KOG0888; Eukaryota.
DR   HOGENOM; CLU_060216_6_3_1; -.
DR   InParanoid; P39207; -.
DR   OMA; FCVQVGK; -.
DR   OrthoDB; 2162449at2759; -.
DR   PhylomeDB; P39207; -.
DR   BioCyc; ARA:AT4G09320-MONOMER; -.
DR   BioCyc; MetaCyc:AT4G09320-MONOMER; -.
DR   BRENDA; 2.7.4.6; 399.
DR   CD-CODE; 4299E36E; Nucleolus.
DR   EvolutionaryTrace; P39207; -.
DR   PRO; PR:P39207; -.
DR   Proteomes; UP000006548; Chromosome 4.
DR   ExpressionAtlas; P39207; baseline and differential.
DR   GO; GO:0048046; C:apoplast; HDA:TAIR.
DR   GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR   GO; GO:0005737; C:cytoplasm; EXP:UniProtKB.
DR   GO; GO:0005829; C:cytosol; HDA:TAIR.
DR   GO; GO:0005634; C:nucleus; EXP:UniProtKB.
DR   GO; GO:0005777; C:peroxisome; IDA:TAIR.
DR   GO; GO:0000325; C:plant-type vacuole; HDA:TAIR.
DR   GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR   GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR   GO; GO:0004550; F:nucleoside diphosphate kinase activity; IDA:UniProtKB.
DR   GO; GO:0070301; P:cellular response to hydrogen peroxide; IDA:UniProtKB.
DR   GO; GO:0006241; P:CTP biosynthetic process; IEA:InterPro.
DR   GO; GO:0006183; P:GTP biosynthetic process; IEA:InterPro.
DR   GO; GO:0009142; P:nucleoside triphosphate biosynthetic process; IBA:GO_Central.
DR   GO; GO:0006228; P:UTP biosynthetic process; IEA:InterPro.
DR   CDD; cd04413; NDPk_I; 1.
DR   FunFam; 3.30.70.141:FF:000002; Nucleoside diphosphate kinase; 1.
DR   Gene3D; 3.30.70.141; Nucleoside diphosphate kinase-like domain; 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   NCBIfam; NF001908; PRK00668.1; 1.
DR   PANTHER; PTHR11349; NUCLEOSIDE DIPHOSPHATE KINASE; 1.
DR   Pfam; PF00334; NDK; 1.
DR   PRINTS; PR01243; NUCDPKINASE.
DR   SMART; SM00562; NDK; 1.
DR   SUPFAM; SSF54919; Nucleoside diphosphate kinase, NDK; 1.
DR   PROSITE; PS00469; NDPK; 1.
DR   PROSITE; PS51374; NDPK_LIKE; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Acetylation; ATP-binding; Cytoplasm; Kinase; Magnesium;
KW   Metal-binding; Nucleotide metabolism; Nucleotide-binding; Nucleus;
KW   Peroxisome; Reference proteome; Stress response; Transferase.
FT   CHAIN           1..149
FT                   /note="Nucleoside diphosphate kinase 1"
FT                   /id="PRO_0000137134"
FT   ACT_SITE        115
FT                   /note="Pros-phosphohistidine intermediate"
FT                   /evidence="ECO:0000250"
FT   BINDING         9
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         57
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         85
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         91
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         102
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         112
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         1
FT                   /note="N-acetylmethionine"
FT                   /evidence="ECO:0007744|PubMed:22223895"
FT   CONFLICT        30..31
FT                   /note="FT -> LH (in Ref. 7; CAA79265)"
FT                   /evidence="ECO:0000305"
FT   STRAND          3..8
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   HELIX           10..14
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   HELIX           18..28
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   STRAND          31..38
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   HELIX           42..48
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   STRAND          53..55
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   HELIX           58..65
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   STRAND          70..77
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   HELIX           80..88
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   TURN            93..95
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   HELIX           101..105
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   STRAND          113..116
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   HELIX           120..130
FT                   /evidence="ECO:0007829|PDB:1U8W"
FT   HELIX           143..145
FT                   /evidence="ECO:0007829|PDB:1U8W"
SQ   SEQUENCE   149 AA;  16500 MW;  21DF53932A07B0BA CRC64;
     MEQTFIMIKP DGVQRGLIGE VICRFEKKGF TLKGLKLISV ERSFAEKHYE DLSSKSFFSG
     LVDYIVSGPV VAMIWEGKNV VLTGRKIIGA TNPAASEPGT IRGDFAIDIG RNVIHGSDSV
     ESARKEIALW FPDGPVNWQS SVHPWVYET
//