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Protein

Nucleoside diphosphate kinase 1

Gene

NDK1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 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. Plays a role in response to reactive oxygen species (ROS) stress.1 Publication

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

  • ATP binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • nucleoside diphosphate kinase activity Source: UniProtKB

GO - Biological processi

  • cellular response to hydrogen peroxide Source: UniProtKB
  • CTP biosynthetic process Source: InterPro
  • GTP biosynthetic process Source: InterPro
  • nucleoside diphosphate phosphorylation Source: UniProtKB
  • UTP biosynthetic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Nucleotide metabolism, Stress response

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciARA:AT4G09320-MONOMER.
MetaCyc:AT4G09320-MONOMER.

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:NDK1
Synonyms:NDPK1
Ordered Locus Names:At4g09320
ORF Names:T30A10.80
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G09320.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 149149Nucleoside diphosphate kinase 1PRO_0000137134Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineCombined sources

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP39207.
PRIDEiP39207.
ProMEXiP39207.

2D gel databases

SWISS-2DPAGEP39207.

PTM databases

iPTMnetiP39207.

Expressioni

Gene expression databases

GenevisibleiP39207. AT.

Interactioni

Subunit structurei

Interacts with CAT1, CAT2 and CAT3.1 Publication

Protein-protein interaction databases

BioGridi11814. 7 interactions.
IntActiP39207. 4 interactions.
STRINGi3702.AT4G09320.1.

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
Beta strandi53 – 553Combined sources
Helixi58 – 658Combined sources
Beta strandi70 – 778Combined sources
Helixi80 – 889Combined sources
Turni93 – 953Combined sources
Helixi101 – 1055Combined sources
Beta strandi113 – 1164Combined sources
Helixi120 – 13011Combined sources
Helixi143 – 1453Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1U8WX-ray2.40A/B/C/D/E/F1-149[»]
ProteinModelPortaliP39207.
SMRiP39207. Positions 1-149.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39207.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
HOGENOMiHOG000224564.
InParanoidiP39207.
KOiK00940.
PhylomeDBiP39207.

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.

P39207-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEQTFIMIKP DGVQRGLIGE VICRFEKKGF TLKGLKLISV ERSFAEKHYE
60 70 80 90 100
DLSSKSFFSG LVDYIVSGPV VAMIWEGKNV VLTGRKIIGA TNPAASEPGT
110 120 130 140
IRGDFAIDIG RNVIHGSDSV ESARKEIALW FPDGPVNWQS SVHPWVYET
Length:149
Mass (Da):16,500
Last modified:February 1, 1995 - v1
Checksum:i21DF53932A07B0BA
GO

Sequence cautioni

The sequence AAK48956.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AEE82742.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence CAA49173.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti30 – 312FT → LH in CAA79265 (PubMed:8281187).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69373 mRNA. Translation: CAA49170.1.
X69376 Genomic DNA. Translation: CAA49173.1. Sequence problems.
AF017641 mRNA. Translation: AAC17844.1.
AL117386 Genomic DNA. Translation: CAB55695.1.
AL161514 Genomic DNA. Translation: CAB78055.1.
CP002687 Genomic DNA. Translation: AEE82742.1. Different initiation.
AF370529 mRNA. Translation: AAK48956.1. Different initiation.
AY072518 mRNA. Translation: AAL66933.1.
Z18791 mRNA. Translation: CAA79265.1.
PIRiS31444.
S31446.
T17131.
RefSeqiNP_567346.1. NM_117000.2.
UniGeneiAt.5402.
At.75255.

Genome annotation databases

EnsemblPlantsiAT4G09320.1; AT4G09320.1; AT4G09320.
GeneIDi826515.
GrameneiAT4G09320.1; AT4G09320.1; AT4G09320.
KEGGiath:AT4G09320.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69373 mRNA. Translation: CAA49170.1.
X69376 Genomic DNA. Translation: CAA49173.1. Sequence problems.
AF017641 mRNA. Translation: AAC17844.1.
AL117386 Genomic DNA. Translation: CAB55695.1.
AL161514 Genomic DNA. Translation: CAB78055.1.
CP002687 Genomic DNA. Translation: AEE82742.1. Different initiation.
AF370529 mRNA. Translation: AAK48956.1. Different initiation.
AY072518 mRNA. Translation: AAL66933.1.
Z18791 mRNA. Translation: CAA79265.1.
PIRiS31444.
S31446.
T17131.
RefSeqiNP_567346.1. NM_117000.2.
UniGeneiAt.5402.
At.75255.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1U8WX-ray2.40A/B/C/D/E/F1-149[»]
ProteinModelPortaliP39207.
SMRiP39207. Positions 1-149.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi11814. 7 interactions.
IntActiP39207. 4 interactions.
STRINGi3702.AT4G09320.1.

PTM databases

iPTMnetiP39207.

2D gel databases

SWISS-2DPAGEP39207.

Proteomic databases

PaxDbiP39207.
PRIDEiP39207.
ProMEXiP39207.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G09320.1; AT4G09320.1; AT4G09320.
GeneIDi826515.
GrameneiAT4G09320.1; AT4G09320.1; AT4G09320.
KEGGiath:AT4G09320.

Organism-specific databases

TAIRiAT4G09320.

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
HOGENOMiHOG000224564.
InParanoidiP39207.
KOiK00940.
PhylomeDBiP39207.

Enzyme and pathway databases

BioCyciARA:AT4G09320-MONOMER.
MetaCyc:AT4G09320-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP39207.
PROiP39207.

Gene expression databases

GenevisibleiP39207. AT.

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. Quigley F.R.
    Submitted (NOV-1992) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
    Strain: cv. C24 and cv. Columbia.
  2. "Cloning and characterization of a phytochrome interacting protein."
    Yi H., Shin B., Lee J., Song P.-S., Choi G.
    Submitted (AUG-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Columbia.
  3. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 4-149.
    Strain: cv. Columbia.
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 5-81.
    Strain: cv. Columbia.
    Tissue: Flower.
  7. "Arabidopsis NDK1 is a component of ROS signaling by interacting with three catalases."
    Fukamatsu Y., Yabe N., Hasunuma K.
    Plant Cell Physiol. 44:982-989(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH CAT1; CAT2 AND CAT3.
  8. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling."
    Im Y.J., Kim J.I., Shen Y., Na Y., Han Y.J., Kim S.H., Song P.S., Eom S.H.
    J. Mol. Biol. 343:659-670(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS).

Entry informationi

Entry nameiNDK1_ARATH
AccessioniPrimary (citable) accession number: P39207
Secondary accession number(s): F4JJZ8, Q41989, Q94JY5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: February 17, 2016
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Plants over-expressing NDK1 are more tolerant to paraquat and have increased ability to eliminate exogenous H2O2.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.