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Protein

Nucleoside diphosphate kinase 1

Gene

NDKR

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. This NDK is microtubule-associated.

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei9 – 91ATPBy similarity
Binding sitei57 – 571ATPBy similarity
Binding sitei85 – 851ATPBy similarity
Binding sitei91 – 911ATPBy similarity
Binding sitei102 – 1021ATPBy similarity
Binding sitei112 – 1121ATPBy similarity
Active sitei115 – 1151Pros-phosphohistidine intermediateBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Nucleotide metabolism

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi2.7.4.6. 4460.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinase 1 (EC:2.7.4.6)
Alternative name(s):
Nucleoside diphosphate kinase I
Short name:
NDK I
Short name:
NDP kinase I
Short name:
NDPK I
Gene namesi
Name:NDKR
Ordered Locus Names:Os07g0492000, LOC_Os07g30970
ORF Names:OJ1218_C12.24, OsJ_023347, P0038F10.104
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryza
Proteomesi
  • UP000059680 Componenti: Chromosome 7, cultivar: Nipponbare

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 149149Nucleoside diphosphate kinase 1PRO_0000137141Add
BLAST

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ07661.

Expressioni

Inductioni

By salicylic acid, benzo (1,2,3) thiadiazole-7-carbothioc acid S-methyl ester, jasmonic acid, and abscisic acid.1 Publication

Gene expression databases

GenevisibleiQ07661. OS.

Interactioni

Subunit structurei

Homohexamer.1 Publication

Protein-protein interaction databases

STRINGi39947.LOC_Os07g30970.1.

Structurei

Secondary structure

1
149
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi10 – 145Combined sources
Helixi18 – 2811Combined sources
Beta strandi31 – 388Combined sources
Helixi42 – 487Combined sources
Helixi50 – 523Combined sources
Helixi58 – 669Combined sources
Beta strandi70 – 778Combined sources
Helixi80 – 889Combined sources
Helixi93 – 953Combined sources
Helixi101 – 1055Combined sources
Beta strandi113 – 1164Combined sources
Helixi120 – 13011Combined sources
Helixi143 – 1464Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PKUX-ray2.50A/B/C/D/E/F/G/H/I/J/K/L1-149[»]
ProteinModelPortaliQ07661.
SMRiQ07661. Positions 1-148.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ07661.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
InParanoidiQ07661.
KOiK00940.
OMAiMLSGPVC.

Family and domain databases

HAMAPiMF_00451. NDP_kinase.
InterProiIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q07661-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEQSFIMIKP DGVQRGLIGD IISRFEKKGF YLRGMKFMNV ERSFAQQHYA
60 70 80 90 100
DLSDKPFFPG LVEYIISGPV VAMVWEGKDV VATGRRIIGA TRPWEAAPGT
110 120 130 140
IRADYAVEVG RNVIHGSDSV DNGKKEIALW FPEGLAEWRS NLHPWIYES
Length:149
Mass (Da):16,861
Last modified:October 1, 1994 - v1
Checksum:i6CD140D220B00920
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti31 – 311Y → F in AAT70416 (PubMed:15650338).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D16292 mRNA. Translation: BAA03798.1.
AY649743 mRNA. Translation: AAT70416.1.
AP004051 Genomic DNA. Translation: BAC83301.1.
AP004266 Genomic DNA. Translation: BAD30551.1.
AP008213 Genomic DNA. Translation: BAF21596.1.
AP014963 Genomic DNA. Translation: BAT01561.1.
CM000144 Genomic DNA. Translation: EAZ39864.1.
PIRiS43330.
RefSeqiXP_015647142.1. XM_015791656.1.
UniGeneiOs.146.

Genome annotation databases

EnsemblPlantsiOS07T0492000-01; OS07T0492000-01; OS07G0492000.
GeneIDi4343275.
GrameneiOS07T0492000-01; OS07T0492000-01; OS07G0492000.
KEGGiosa:4343275.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D16292 mRNA. Translation: BAA03798.1.
AY649743 mRNA. Translation: AAT70416.1.
AP004051 Genomic DNA. Translation: BAC83301.1.
AP004266 Genomic DNA. Translation: BAD30551.1.
AP008213 Genomic DNA. Translation: BAF21596.1.
AP014963 Genomic DNA. Translation: BAT01561.1.
CM000144 Genomic DNA. Translation: EAZ39864.1.
PIRiS43330.
RefSeqiXP_015647142.1. XM_015791656.1.
UniGeneiOs.146.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PKUX-ray2.50A/B/C/D/E/F/G/H/I/J/K/L1-149[»]
ProteinModelPortaliQ07661.
SMRiQ07661. Positions 1-148.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os07g30970.1.

Proteomic databases

PaxDbiQ07661.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiOS07T0492000-01; OS07T0492000-01; OS07G0492000.
GeneIDi4343275.
GrameneiOS07T0492000-01; OS07T0492000-01; OS07G0492000.
KEGGiosa:4343275.

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
InParanoidiQ07661.
KOiK00940.
OMAiMLSGPVC.

Enzyme and pathway databases

BRENDAi2.7.4.6. 4460.

Miscellaneous databases

EvolutionaryTraceiQ07661.

Gene expression databases

GenevisibleiQ07661. OS.

Family and domain databases

HAMAPiMF_00451. NDP_kinase.
InterProiIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning and nucleotide sequence cDNA encoding nucleoside diphosphate kinase of rice (Oryza sativa L.)."
    Yano A., Shimaaki T., Kato A., Umeda M., Uchimiya H.
    Plant Mol. Biol. 23:1087-1090(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Enhanced expression of a gene encoding a nucleoside diphosphate kinase 1 (OsNDPK1) in rice plants upon infection with bacterial pathogens."
    Cho S.M., Shin S.H., Kim K.S., Kim Y.C., Eun M.Y., Cho B.H.
    Mol. Cells 18:390-395(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], INDUCTION.
    Strain: cv. Dongjin.
    Tissue: Leaf.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  4. "The rice annotation project database (RAP-DB): 2008 update."
    The rice annotation project (RAP)
    Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  5. Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  6. "The genomes of Oryza sativa: a history of duplications."
    Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.
    , Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.
    PLoS Biol. 3:266-281(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  7. "Crystal structure of nucleoside diphosphate kinase required for coleoptile elongation in rice (Oryza sativa L.)."
    Huang J.-Y., Chang T., Chang C.-Y., Chen C.-J.
    J. Struct. Biol. 150:309-318(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiNDK1_ORYSJ
AccessioniPrimary (citable) accession number: Q07661
Secondary accession number(s): A0A0P0X6I2
, Q0D6C7, Q6DQV1, Q6ZHK3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: May 11, 2016
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.