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Protein

Nucleoside diphosphate kinase 1

Gene

NDK1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -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

Miscellaneous

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

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei9ATPBy similarity1
Binding sitei57ATPBy similarity1
Binding sitei85ATPBy similarity1
Binding sitei91ATPBy similarity1
Binding sitei102ATPBy similarity1
Binding sitei112ATPBy similarity1
Active sitei115Pros-phosphohistidine intermediateBy similarity1

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

Keywordsi

Molecular functionKinase, Transferase
Biological processNucleotide metabolism, Stress response
LigandATP-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

AraportiAT4G09320

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus, Peroxisome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001371341 – 149Nucleoside diphosphate kinase 1Add BLAST149

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP39207
PRIDEiP39207
ProMEXiP39207

2D gel databases

SWISS-2DPAGEiP39207

PTM databases

iPTMnetiP39207

Expressioni

Gene expression databases

ExpressionAtlasiP39207 baseline and differential
GenevisibleiP39207 AT

Interactioni

Subunit structurei

Interacts with CAT1, CAT2 and CAT3.1 Publication

Protein-protein interaction databases

BioGridi11814, 7 interactors
IntActiP39207, 4 interactors
STRINGi3702.AT4G09320.1

Structurei

Secondary structure

1149
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Helixi10 – 14Combined sources5
Helixi18 – 28Combined sources11
Beta strandi31 – 38Combined sources8
Helixi42 – 48Combined sources7
Beta strandi53 – 55Combined sources3
Helixi58 – 65Combined sources8
Beta strandi70 – 77Combined sources8
Helixi80 – 88Combined sources9
Turni93 – 95Combined sources3
Helixi101 – 105Combined sources5
Beta strandi113 – 116Combined sources4
Helixi120 – 130Combined sources11
Helixi143 – 145Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP39207

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiKOG0888 Eukaryota
COG0105 LUCA
HOGENOMiHOG000224564
InParanoidiP39207
KOiK00940
OrthoDBiEOG09360QL0
PhylomeDBiP39207

Family and domain databases

Gene3Di3.30.70.141, 1 hit
HAMAPiMF_00451 NDP_kinase, 1 hit
InterProiView protein in InterPro
IPR034907 NDK-like_dom
IPR036850 NDK-like_dom_sf
IPR001564 Nucleoside_diP_kinase
IPR023005 Nucleoside_diP_kinase_AS
PfamiView protein in Pfam
PF00334 NDK, 1 hit
PRINTSiPR01243 NUCDPKINASE
SMARTiView protein in SMART
SM00562 NDK, 1 hit
SUPFAMiSSF54919 SSF54919, 1 hit
PROSITEiView protein in PROSITE
PS00469 NDP_KINASES, 1 hit

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti30 – 31FT → LH in CAA79265 (PubMed:8281187).Curated2

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: AEE82742.2
AF370529 mRNA Translation: AAK48956.1 Different initiation.
AY072518 mRNA Translation: AAL66933.1
Z18791 mRNA Translation: CAA79265.1
PIRiS31444
S31446
T17131
RefSeqiNP_567346.2, NM_117000.3
UniGeneiAt.5402
At.75255

Genome annotation databases

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

Similar proteinsi

Entry informationi

Entry nameiNDK1_ARATH
AccessioniPrimary (citable) accession number: P39207
Secondary accession number(s): F4JJZ8, Q41989, Q94JY5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: April 25, 2018
This is version 147 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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

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