Skip Header

Contribute Send feedback
Read comments (?) or add your own

Q07661 (NDK1_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Last modified November 16, 2011. Version 81. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:NDKR
Ordered Locus Names:Os07g0492000, LOC_Os07g30970
ORF Names:OJ1218_C12.24, P0038F10.104, OsJ_023347
OrganismOryza sativa subsp. japonica (Rice)
Taxonomic identifier39947 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza

Protein attributes

Sequence length149 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactor

Magnesium By similarity.

Subunit structure

Homohexamer. Ref.6

Induction

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

Sequence similarities

Belongs to the NDK family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 149149Nucleoside diphosphate kinase 1
PRO_0000137141

Sites

Active site1151Pros-phosphohistidine intermediate By similarity
Binding site91ATP By similarity
Binding site571ATP By similarity
Binding site851ATP By similarity
Binding site911ATP By similarity
Binding site1021ATP By similarity
Binding site1121ATP By similarity

Experimental info

Sequence conflict311Y → F in AAT70416. Ref.2

Secondary structure

1 ............................. 149
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q07661 [UniParc].

Last modified October 1, 1994. Version 1.
Checksum: 6CD140D220B00920

FASTA14916,861
        10         20         30         40         50         60 
MEQSFIMIKP DGVQRGLIGD IISRFEKKGF YLRGMKFMNV ERSFAQQHYA DLSDKPFFPG 

        70         80         90        100        110        120 
LVEYIISGPV VAMVWEGKDV VATGRRIIGA TRPWEAAPGT IRADYAVEVG RNVIHGSDSV 

       130        140 
DNGKKEIALW FPEGLAEWRS NLHPWIYES

« Hide

References

« Hide 'large scale' references
[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: 8260630] [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: 15650338] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], INDUCTION.
Strain: cv. Dongjin.
Tissue: Leaf.
[3]"The map-based sequence of the rice genome."
International rice genome sequencing project (IRGSP)
Nature 436:793-800(2005) [PubMed: 16100779] [Abstract]
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: 18089549] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: cv. Nipponbare.
[5]"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. expand/collapse author list , 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: 15685292] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Nipponbare.
[6]"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: 15890279] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		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.
CM000144 Genomic DNA. Translation: EAZ39864.1.
PIRS43330.
RefSeqNP_001059682.1. NM_001066217.1.
UniGeneOs.146.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1PKUX-ray2.50A/B/C/D/E/F/G/H/I/J/K/L1-149[»]
ProteinModelPortalQ07661.
SMRQ07661. Positions 1-148.
ModBaseSearch...

Protein-protein interaction databases

STRINGQ07661.

2D gel databases

ANU-2DPAGEQ07661.

Proteomic databases

PRIDEQ07661.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsLOC_Os07g30970.1; LOC_Os07g30970.1; LOC_Os07g30970.
GeneID4343275.
KEGGosa:4343275.

Organism-specific databases

GrameneQ07661.

Phylogenomic databases

GeneTreeEPGT00070000028969.
HOGENOMHBG445152.
OMARIIGATR.
PhylomeDBQ07661.
ProtClustDBCLSN2696749.

Family and domain databases

InterProIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
Gene3DG3DSA:3.30.70.141. NDK. 1 hit.
KOK00940.
PANTHERPTHR11349. Nuc_diP_kinase_core. 1 hit.
PfamPF00334. NDK. 1 hit.
[Graphical view]
PRINTSPR01243. NUCDPKINASE.
SMARTSM00562. NDK. 1 hit.
[Graphical view]
SUPFAMSSF54919. NDK. 1 hit.
PROSITEPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameNDK1_ORYSJ
AccessionPrimary (citable) accession number: Q07661
Secondary accession number(s): Q0D6C7, Q6DQV1, Q6ZHK3
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: November 16, 2011
This is version 81 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

Oryza sativa (rice)

Index of Oryza sativa entries and their corresponding gene designations

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents