NDK2_ARATH
ID NDK2_ARATH Reviewed; 231 AA.
AC O64903; O65212; Q9SMX6;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 11-JAN-2001, sequence version 2.
DT 03-AUG-2022, entry version 172.
DE RecName: Full=Nucleoside diphosphate kinase II, chloroplastic;
DE Short=NDK II;
DE Short=NDP kinase II;
DE Short=NDPK II;
DE Short=NDPK Ia;
DE EC=2.7.4.6;
DE Flags: Precursor;
GN Name=NDPK2; OrderedLocusNames=At5g63310; ORFNames=MDC12.28;
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].
RC STRAIN=cv. Columbia;
RA Yi H., Song P.-S., Choi G.;
RT "Cloning and characterization of nucleoside diphosphate kinase 2 from
RT Arabidopsis thaliana.";
RL (er) Plant Gene Register PGR98-056(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=10358052; DOI=10.1074/jbc.274.24.17017;
RA Zimmermann S., Baumann A., Jaekel K., Marbach I., Engelberg D.,
RA Frohnmeyer H.;
RT "UV responsive genes of Arabidopsis revealed by similarity to the Gcn4
RT mediated UV response in yeast.";
RL J. Biol. Chem. 274:17017-17024(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9501997; DOI=10.1093/dnares/4.6.401;
RA Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence
RT features of the regions of 1,191,918 bp covered by seventeen physically
RT assigned P1 clones.";
RL DNA Res. 4:401-414(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
RN [5]
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 [6]
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 [7]
RP FUNCTION, INDUCTION, PHOSPHORYLATION, AND INTERACTION WITH MPK3 AND MPK6.
RX PubMed=12506203; DOI=10.1073/pnas.252641899;
RA Moon H., Lee B., Choi G., Shin D., Prasad D.T., Lee O., Kwak S.-S.,
RA Kim D.H., Nam J., Bahk J., Hong J.C., Lee S.Y., Cho M.J., Lim C.O.,
RA Yun D.-J.;
RT "NDP kinase 2 interacts with two oxidative stress-activated MAPKs to
RT regulate cellular redox state and enhances multiple stress tolerance in
RT transgenic plants.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:358-363(2003).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=18431481; DOI=10.1371/journal.pone.0001994;
RA Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q.,
RA van Wijk K.J.;
RT "Sorting signals, N-terminal modifications and abundance of the chloroplast
RT proteome.";
RL PLoS ONE 3:E1994-E1994(2008).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 79-231 IN COMPLEX WITH ATP ANALOG,
RP AND INTERACTION WITH PHYA.
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. May activate MPK3 and MPK6. May be involved in the
CC regulation of cellular redox state and hydrogen peroxide-mediated MAP
CC kinase signaling. {ECO:0000269|PubMed:12506203}.
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 PHYA, MPK3 and MPK6.
CC {ECO:0000269|PubMed:12506203, ECO:0000269|PubMed:15465053}.
CC -!- INTERACTION:
CC O64903; Q9LDI3: CIPK24; NbExp=3; IntAct=EBI-349517, EBI-537551;
CC O64903; Q39023: MPK3; NbExp=4; IntAct=EBI-349517, EBI-349526;
CC O64903; P14712: PHYA; NbExp=3; IntAct=EBI-349517, EBI-624446;
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:18431481}.
CC -!- INDUCTION: By hydrogen peroxide. {ECO:0000269|PubMed:12506203}.
CC -!- PTM: Autophosphorylated. {ECO:0000269|PubMed:12506203}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
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DR EMBL; AF017640; AAC15253.1; -; mRNA.
DR EMBL; AJ012758; CAB58230.1; -; mRNA.
DR EMBL; AB008265; BAB10573.1; -; Genomic_DNA.
DR EMBL; AB023035; BAB10573.1; JOINED; Genomic_DNA.
DR EMBL; CP002688; AED97731.1; -; Genomic_DNA.
DR EMBL; AY057612; AAL14407.1; -; mRNA.
DR EMBL; AY065291; AAL38767.1; -; mRNA.
DR EMBL; AY117366; AAM51441.1; -; mRNA.
DR EMBL; AF058391; AAC14280.1; -; mRNA.
DR PIR; T51612; T51612.
DR PIR; T52586; T52586.
DR RefSeq; NP_568970.2; NM_125726.4.
DR PDB; 1S57; X-ray; 1.80 A; A/B/C/D/E/F=79-231.
DR PDB; 1S59; X-ray; 2.60 A; A/B/C/D/E/F=79-231.
DR PDBsum; 1S57; -.
DR PDBsum; 1S59; -.
DR AlphaFoldDB; O64903; -.
DR SMR; O64903; -.
DR BioGRID; 21694; 21.
DR IntAct; O64903; 14.
DR STRING; 3702.AT5G63310.1; -.
DR iPTMnet; O64903; -.
DR PaxDb; O64903; -.
DR PRIDE; O64903; -.
DR ProteomicsDB; 251000; -.
DR EnsemblPlants; AT5G63310.1; AT5G63310.1; AT5G63310.
DR GeneID; 836451; -.
DR Gramene; AT5G63310.1; AT5G63310.1; AT5G63310.
DR KEGG; ath:AT5G63310; -.
DR Araport; AT5G63310; -.
DR TAIR; locus:2161922; AT5G63310.
DR eggNOG; KOG0888; Eukaryota.
DR HOGENOM; CLU_060216_4_1_1; -.
DR InParanoid; O64903; -.
DR OMA; LLNWECC; -.
DR OrthoDB; 1334716at2759; -.
DR PhylomeDB; O64903; -.
DR BioCyc; ARA:AT5G63310-MON; -.
DR BRENDA; 2.7.4.6; 399.
DR EvolutionaryTrace; O64903; -.
DR PRO; PR:O64903; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; O64903; baseline and differential.
DR Genevisible; O64903; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0009579; C:thylakoid; HDA:TAIR.
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:TAIR.
DR GO; GO:0009734; P:auxin-activated signaling pathway; IMP: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:0009585; P:red, far-red light phototransduction; IMP:TAIR.
DR GO; GO:0042542; P:response to hydrogen peroxide; IMP:TAIR.
DR GO; GO:0009411; P:response to UV; TAS:TAIR.
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; ATP-binding; Chloroplast; Kinase; Magnesium; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Phosphoprotein; Plastid;
KW Reference proteome; Transferase; Transit peptide.
FT TRANSIT 1..62
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 63..231
FT /note="Nucleoside diphosphate kinase II, chloroplastic"
FT /id="PRO_0000019434"
FT ACT_SITE 197
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 91
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 139
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 167
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 173
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 184
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 194
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT CONFLICT 133
FT /note="D -> E (in Ref. 1; AAC15253)"
FT /evidence="ECO:0000305"
FT CONFLICT 141..142
FT /note="PN -> LT (in Ref. 1; AAC15253)"
FT /evidence="ECO:0000305"
FT STRAND 84..90
FT /evidence="ECO:0007829|PDB:1S57"
FT HELIX 92..96
FT /evidence="ECO:0007829|PDB:1S57"
FT HELIX 100..110
FT /evidence="ECO:0007829|PDB:1S57"
FT STRAND 113..120
FT /evidence="ECO:0007829|PDB:1S57"
FT HELIX 124..130
FT /evidence="ECO:0007829|PDB:1S57"
FT HELIX 132..134
FT /evidence="ECO:0007829|PDB:1S57"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:1S57"
FT HELIX 140..147
FT /evidence="ECO:0007829|PDB:1S57"
FT STRAND 152..159
FT /evidence="ECO:0007829|PDB:1S57"
FT HELIX 162..170
FT /evidence="ECO:0007829|PDB:1S57"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:1S57"
FT HELIX 183..187
FT /evidence="ECO:0007829|PDB:1S57"
FT HELIX 191..193
FT /evidence="ECO:0007829|PDB:1S59"
FT STRAND 196..198
FT /evidence="ECO:0007829|PDB:1S57"
FT HELIX 202..212
FT /evidence="ECO:0007829|PDB:1S57"
FT HELIX 226..229
FT /evidence="ECO:0007829|PDB:1S57"
SQ SEQUENCE 231 AA; 25550 MW; E9EE97A77942E5EA CRC64;
MVGATVVSKW TPLCVASPPE RNSASLNPHC SPARVNFRTA LAAFRPQFRL FSRNSASRRR
LRASSSAESG IFLPHLVASM EDVEETYIMV KPDGIQRGLV GEIISRFEKK GFKLIGLKMF
QCPKELAEEH YKDLSAKSFF PNLIEYITSG PVVCMAWEGV GVVASARKLI GKTDPLQAEP
GTIRGDLAVQ TGRNIVHGSD SPENGKREIG LWFKEGELCK WDSALATWLR E
