NDK1_ARATH
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 03-AUG-2022, entry version 166.
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; 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 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 [6]
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 [7]
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 [8]
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 [9]
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 [10]
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; 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 PDBsum; 1U8W; -.
DR AlphaFoldDB; P39207; -.
DR SMR; P39207; -.
DR BioGRID; 11814; 19.
DR IntAct; P39207; 4.
DR STRING; 3702.AT4G09320.1; -.
DR iPTMnet; P39207; -.
DR SWISS-2DPAGE; P39207; -.
DR PaxDb; P39207; -.
DR PRIDE; P39207; -.
DR ProMEX; P39207; -.
DR ProteomicsDB; 251129; -.
DR EnsemblPlants; AT4G09320.1; AT4G09320.1; AT4G09320.
DR GeneID; 826515; -.
DR Gramene; AT4G09320.1; AT4G09320.1; AT4G09320.
DR KEGG; ath:AT4G09320; -.
DR Araport; AT4G09320; -.
DR eggNOG; KOG0888; Eukaryota.
DR HOGENOM; CLU_060216_6_3_1; -.
DR InParanoid; P39207; -.
DR OMA; KIVAMKM; -.
DR OrthoDB; 1334716at2759; -.
DR PhylomeDB; P39207; -.
DR BioCyc; ARA:AT4G09320-MON; -.
DR BioCyc; MetaCyc:AT4G09320-MON; -.
DR BRENDA; 2.7.4.6; 399.
DR EvolutionaryTrace; P39207; -.
DR PRO; PR:P39207; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; P39207; baseline and differential.
DR Genevisible; P39207; AT.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0005777; C:peroxisome; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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:0006165; P:nucleoside diphosphate phosphorylation; IDA:UniProtKB.
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 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. 6; 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
