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Protein

Nucleoside diphosphate kinase II, chloroplastic

Gene

NDPK2

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. May activate MPK3 and MPK6. May be involved in the regulation of cellular redox state and hydrogen peroxide-mediated MAP kinase signaling.1 Publication

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei91 – 911ATP
Binding sitei139 – 1391ATP
Binding sitei167 – 1671ATP
Binding sitei173 – 1731ATP
Binding sitei184 – 1841ATP
Binding sitei194 – 1941ATP
Active sitei197 – 1971Pros-phosphohistidine intermediateBy similarity

GO - Molecular functioni

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

GO - Biological processi

  • auxin-activated signaling pathway Source: TAIR
  • CTP biosynthetic process Source: InterPro
  • GTP biosynthetic process Source: InterPro
  • nucleoside triphosphate biosynthetic process Source: GO_Central
  • purine nucleotide metabolic process Source: GO_Central
  • pyrimidine nucleotide metabolic process Source: GO_Central
  • red, far-red light phototransduction Source: TAIR
  • response to hydrogen peroxide Source: TAIR
  • response to UV Source: TAIR
  • UTP biosynthetic process Source: InterPro
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

BioCyciARA:AT5G63310-MONOMER.
BRENDAi2.7.4.6. 399.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinase II, chloroplastic (EC:2.7.4.6)
Short name:
NDK II
Short name:
NDP kinase II
Short name:
NDPK II
Short name:
NDPK Ia
Gene namesi
Name:NDPK2
Ordered Locus Names:At5g63310
ORF Names:MDC12.28
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G63310.

Subcellular locationi

GO - Cellular componenti

  • chloroplast Source: TAIR
  • chloroplast envelope Source: TAIR
  • chloroplast stroma Source: TAIR
  • cytoplasm Source: TAIR
  • nucleus Source: TAIR
  • thylakoid Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 6262ChloroplastSequence analysisAdd
BLAST
Chaini63 – 231169Nucleoside diphosphate kinase II, chloroplasticPRO_0000019434Add
BLAST

Post-translational modificationi

Autophosphorylated.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiO64903.
PRIDEiO64903.

PTM databases

iPTMnetiO64903.

Expressioni

Inductioni

By hydrogen peroxide.1 Publication

Gene expression databases

ExpressionAtlasiO64903. baseline and differential.
GenevisibleiO64903. AT.

Interactioni

Subunit structurei

Interacts with PHYA, MPK3 and MPK6.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CIPK24Q9LDI33EBI-349517,EBI-537551
MPK3Q390234EBI-349517,EBI-349526
PHYAP147123EBI-349517,EBI-624446

Protein-protein interaction databases

BioGridi21694. 14 interactions.
IntActiO64903. 13 interactions.
STRINGi3702.AT5G63310.1.

Structurei

Secondary structure

1
231
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi84 – 907Combined sources
Helixi92 – 965Combined sources
Helixi100 – 11011Combined sources
Beta strandi113 – 1208Combined sources
Helixi124 – 1307Combined sources
Helixi132 – 1343Combined sources
Beta strandi137 – 1393Combined sources
Helixi140 – 1478Combined sources
Beta strandi152 – 1598Combined sources
Helixi162 – 1709Combined sources
Turni175 – 1773Combined sources
Helixi183 – 1875Combined sources
Helixi191 – 1933Combined sources
Beta strandi196 – 1983Combined sources
Helixi202 – 21211Combined sources
Helixi226 – 2294Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1S57X-ray1.80A/B/C/D/E/F79-231[»]
1S59X-ray2.60A/B/C/D/E/F79-231[»]
ProteinModelPortaliO64903.
SMRiO64903. Positions 79-231.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO64903.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
HOGENOMiHOG000224564.
InParanoidiO64903.
KOiK00940.
OMAiELAQWES.
OrthoDBiEOG09360OX1.
PhylomeDBiO64903.

Family and domain databases

HAMAPiMF_00451. NDP_kinase. 1 hit.
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.

Sequence processingi: The displayed sequence is further processed into a mature form.

O64903-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVGATVVSKW TPLCVASPPE RNSASLNPHC SPARVNFRTA LAAFRPQFRL
60 70 80 90 100
FSRNSASRRR LRASSSAESG IFLPHLVASM EDVEETYIMV KPDGIQRGLV
110 120 130 140 150
GEIISRFEKK GFKLIGLKMF QCPKELAEEH YKDLSAKSFF PNLIEYITSG
160 170 180 190 200
PVVCMAWEGV GVVASARKLI GKTDPLQAEP GTIRGDLAVQ TGRNIVHGSD
210 220 230
SPENGKREIG LWFKEGELCK WDSALATWLR E
Length:231
Mass (Da):25,550
Last modified:January 11, 2001 - v2
Checksum:iE9EE97A77942E5EA
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti133 – 1331D → E in AAC15253 (Ref. 1) Curated
Sequence conflicti141 – 1422PN → LT in AAC15253 (Ref. 1) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF017640 mRNA. Translation: AAC15253.1.
AJ012758 mRNA. Translation: CAB58230.1.
AB008265, AB023035 Genomic DNA. Translation: BAB10573.1.
CP002688 Genomic DNA. Translation: AED97731.1.
AY057612 mRNA. Translation: AAL14407.1.
AY065291 mRNA. Translation: AAL38767.1.
AY117366 mRNA. Translation: AAM51441.1.
AF058391 mRNA. Translation: AAC14280.1.
PIRiT51612.
T52586.
RefSeqiNP_568970.2. NM_125726.3.
UniGeneiAt.24504.

Genome annotation databases

EnsemblPlantsiAT5G63310.1; AT5G63310.1; AT5G63310.
GeneIDi836451.
GrameneiAT5G63310.1; AT5G63310.1; AT5G63310.
KEGGiath:AT5G63310.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF017640 mRNA. Translation: AAC15253.1.
AJ012758 mRNA. Translation: CAB58230.1.
AB008265, AB023035 Genomic DNA. Translation: BAB10573.1.
CP002688 Genomic DNA. Translation: AED97731.1.
AY057612 mRNA. Translation: AAL14407.1.
AY065291 mRNA. Translation: AAL38767.1.
AY117366 mRNA. Translation: AAM51441.1.
AF058391 mRNA. Translation: AAC14280.1.
PIRiT51612.
T52586.
RefSeqiNP_568970.2. NM_125726.3.
UniGeneiAt.24504.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1S57X-ray1.80A/B/C/D/E/F79-231[»]
1S59X-ray2.60A/B/C/D/E/F79-231[»]
ProteinModelPortaliO64903.
SMRiO64903. Positions 79-231.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi21694. 14 interactions.
IntActiO64903. 13 interactions.
STRINGi3702.AT5G63310.1.

PTM databases

iPTMnetiO64903.

Proteomic databases

PaxDbiO64903.
PRIDEiO64903.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G63310.1; AT5G63310.1; AT5G63310.
GeneIDi836451.
GrameneiAT5G63310.1; AT5G63310.1; AT5G63310.
KEGGiath:AT5G63310.

Organism-specific databases

TAIRiAT5G63310.

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
HOGENOMiHOG000224564.
InParanoidiO64903.
KOiK00940.
OMAiELAQWES.
OrthoDBiEOG09360OX1.
PhylomeDBiO64903.

Enzyme and pathway databases

BioCyciARA:AT5G63310-MONOMER.
BRENDAi2.7.4.6. 399.

Miscellaneous databases

EvolutionaryTraceiO64903.
PROiO64903.

Gene expression databases

ExpressionAtlasiO64903. baseline and differential.
GenevisibleiO64903. AT.

Family and domain databases

HAMAPiMF_00451. NDP_kinase. 1 hit.
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...

Entry informationi

Entry nameiNDK2_ARATH
AccessioniPrimary (citable) accession number: O64903
Secondary accession number(s): O65212, Q9SMX6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 11, 2001
Last modified: September 7, 2016
This is version 138 of the entry and version 2 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. 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.