NDK1_ORYSJ
ID NDK1_ORYSJ Reviewed; 149 AA.
AC Q07661; A0A0P0X6I2; Q0D6C7; Q6DQV1; Q6ZHK3;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 145.
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=NDKR; OrderedLocusNames=Os07g0492000, LOC_Os07g30970;
GN ORFNames=OJ1218_C12.24, OsJ_023347, P0038F10.104;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=8260630; DOI=10.1007/bf00021824;
RA Yano A., Shimaaki T., Kato A., Umeda M., Uchimiya H.;
RT "Molecular cloning and nucleotide sequence cDNA encoding nucleoside
RT diphosphate kinase of rice (Oryza sativa L.).";
RL Plant Mol. Biol. 23:1087-1090(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], AND INDUCTION.
RC STRAIN=cv. Dongjin; TISSUE=Leaf;
RX PubMed=15650338;
RA Cho S.M., Shin S.H., Kim K.S., Kim Y.C., Eun M.Y., Cho B.H.;
RT "Enhanced expression of a gene encoding a nucleoside diphosphate kinase 1
RT (OsNDPK1) in rice plants upon infection with bacterial pathogens.";
RL Mol. Cells 18:390-395(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), AND SUBUNIT.
RX PubMed=15890279; DOI=10.1016/j.jsb.2005.02.010;
RA Huang J.-Y., Chang T., Chang C.-Y., Chen C.-J.;
RT "Crystal structure of nucleoside diphosphate kinase required for coleoptile
RT elongation in rice (Oryza sativa L.).";
RL J. Struct. Biol. 150:309-318(2005).
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. This NDK is microtubule-associated.
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:0000269|PubMed:15890279}.
CC -!- INDUCTION: By salicylic acid, benzo (1,2,3) thiadiazole-7-carbothioc
CC acid S-methyl ester, jasmonic acid, and abscisic acid.
CC {ECO:0000269|PubMed:15650338}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
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DR EMBL; D16292; BAA03798.1; -; mRNA.
DR EMBL; AY649743; AAT70416.1; -; mRNA.
DR EMBL; AP004051; BAC83301.1; -; Genomic_DNA.
DR EMBL; AP004266; BAD30551.1; -; Genomic_DNA.
DR EMBL; AP008213; BAF21596.1; -; Genomic_DNA.
DR EMBL; AP014963; BAT01561.1; -; Genomic_DNA.
DR EMBL; CM000144; EAZ39864.1; -; Genomic_DNA.
DR PIR; S43330; S43330.
DR RefSeq; XP_015647142.1; XM_015791656.1.
DR PDB; 1PKU; X-ray; 2.50 A; A/B/C/D/E/F/G/H/I/J/K/L=1-149.
DR PDBsum; 1PKU; -.
DR AlphaFoldDB; Q07661; -.
DR SMR; Q07661; -.
DR STRING; 4530.OS07T0492000-01; -.
DR PaxDb; Q07661; -.
DR PRIDE; Q07661; -.
DR EnsemblPlants; Os07t0492000-01; Os07t0492000-01; Os07g0492000.
DR GeneID; 4343275; -.
DR Gramene; Os07t0492000-01; Os07t0492000-01; Os07g0492000.
DR KEGG; osa:4343275; -.
DR eggNOG; KOG0888; Eukaryota.
DR HOGENOM; CLU_060216_6_3_1; -.
DR InParanoid; Q07661; -.
DR OMA; SAKIEMQ; -.
DR OrthoDB; 1334716at2759; -.
DR BRENDA; 2.7.4.6; 4460.
DR EvolutionaryTrace; Q07661; -.
DR Proteomes; UP000000763; Chromosome 7.
DR Proteomes; UP000007752; Chromosome 7.
DR Proteomes; UP000059680; Chromosome 7.
DR Genevisible; Q07661; OS.
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; IBA:GO_Central.
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 3D-structure; ATP-binding; Kinase; Magnesium; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Phosphoprotein;
KW Reference proteome; Transferase.
FT CHAIN 1..149
FT /note="Nucleoside diphosphate kinase 1"
FT /id="PRO_0000137141"
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 CONFLICT 31
FT /note="Y -> F (in Ref. 2; AAT70416)"
FT /evidence="ECO:0000305"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:1PKU"
FT HELIX 10..14
FT /evidence="ECO:0007829|PDB:1PKU"
FT HELIX 18..28
FT /evidence="ECO:0007829|PDB:1PKU"
FT STRAND 31..38
FT /evidence="ECO:0007829|PDB:1PKU"
FT HELIX 42..48
FT /evidence="ECO:0007829|PDB:1PKU"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:1PKU"
FT HELIX 58..66
FT /evidence="ECO:0007829|PDB:1PKU"
FT STRAND 70..77
FT /evidence="ECO:0007829|PDB:1PKU"
FT HELIX 80..88
FT /evidence="ECO:0007829|PDB:1PKU"
FT HELIX 93..95
FT /evidence="ECO:0007829|PDB:1PKU"
FT HELIX 101..105
FT /evidence="ECO:0007829|PDB:1PKU"
FT STRAND 113..116
FT /evidence="ECO:0007829|PDB:1PKU"
FT HELIX 120..130
FT /evidence="ECO:0007829|PDB:1PKU"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:1PKU"
SQ SEQUENCE 149 AA; 16861 MW; 6CD140D220B00920 CRC64;
MEQSFIMIKP DGVQRGLIGD IISRFEKKGF YLRGMKFMNV ERSFAQQHYA DLSDKPFFPG
LVEYIISGPV VAMVWEGKDV VATGRRIIGA TRPWEAAPGT IRADYAVEVG RNVIHGSDSV
DNGKKEIALW FPEGLAEWRS NLHPWIYES
