O64903 (NDK2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Nucleoside diphosphate kinase II, chloroplastic
Short name=NDK II
Short name=NDP kinase II
Short name=NDPK II
Short name=NDPK Ia
EC=2.7.4.6

Gene names

Name:	NDPK2
Ordered Locus Names:	At5g63310
ORF Names:	MDC12.28

Organism

Arabidopsis thaliana (Mouse-ear cress)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	231 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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. May activate MPK3 and MPK6. May be involved in the regulation of cellular redox state and hydrogen peroxide-mediated MAP kinase signaling. Ref.7
Catalytic activity	ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
Cofactor	Magnesium By similarity.
Subunit structure	Interacts with PHYA, MPK3 and MPK6. Ref.7 Ref.11
Subcellular location	Plastid › chloroplast Ref.8 Ref.9.
Induction	By hydrogen peroxide. Ref.7
Post-translational modification	Autophosphorylated. Ref.7 Ref.10
Sequence similarities	Belongs to the NDK family.

Ontologies

Keywords
Biological process	Nucleotide metabolism
Cellular component	Chloroplast Plastid
Domain	Transit peptide
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	CTP biosynthetic process Inferred from electronic annotation. Source: InterPro GTP biosynthetic process Inferred from electronic annotation. Source: InterPro UTP biosynthetic process Inferred from electronic annotation. Source: InterPro auxin mediated signaling pathway Inferred from mutant phenotype. Source: TAIR red, far-red light phototransduction Inferred from mutant phenotype. Source: TAIR response to UV Traceable author statement. Source: TAIR response to hydrogen peroxide Inferred from expression pattern Ref.7. Source: TAIR
Cellular component	chloroplast envelope Inferred from direct assay. Source: TAIR chloroplast stroma Inferred from direct assay Ref.8. Source: TAIR nucleus Inferred from direct assay Ref.2. Source: TAIR thylakoid Inferred from direct assay. Source: TAIR
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside diphosphate kinase activity Inferred from direct assay Ref.11. Source: TAIR protein binding Inferred from physical interaction Ref.7. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CIPK24	Q9LDI3	3	EBI-349517,EBI-537551
MPK3	Q39023	4	EBI-349517,EBI-349526
PHYA	P14712	3	EBI-349517,EBI-624446

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 62

62

Chloroplast Potential

Chain

63 – 231

169

Nucleoside diphosphate kinase II, chloroplastic

PRO_0000019434

Sites

Active site

197

1

Pros-phosphohistidine intermediate By similarity

Binding site

91

1

ATP

Binding site

139

1

ATP

Binding site

167

1

ATP

Binding site

173

1

ATP

Binding site

184

1

ATP

Binding site

194

1

ATP

Amino acid modifications

Modified residue

201

1

Phosphoserine Ref.10

Experimental info

Sequence conflict

133

1

D → E in AAC15253. Ref.1

Sequence conflict

141 – 142

2

PN → LT in AAC15253. Ref.1

Secondary structure

1

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231

Helix Strand Turn

Details...

Beta strand

84 – 90

7

Helix

92 – 96

5

Helix

100 – 110

11

Beta strand

113 – 120

8

Helix

124 – 130

7

Helix

132 – 134

3

Beta strand

137 – 139

3

Helix

140 – 147

8

Beta strand

152 – 159

8

Helix

162 – 170

9

Turn

175 – 177

3

Helix

183 – 187

5

Beta strand

196 – 198

3

Helix

202 – 212

11

Helix

226 – 229

4

Sequences

	Sequence		Length	Mass (Da)
	O64903 [UniParc]. Last modified January 11, 2001. Version 2. Checksum: E9EE97A77942E5EA	FASTA	231	25,550
	10 20 30 40 50 60 MVGATVVSKW TPLCVASPPE RNSASLNPHC SPARVNFRTA LAAFRPQFRL FSRNSASRRR 70 80 90 100 110 120 LRASSSAESG IFLPHLVASM EDVEETYIMV KPDGIQRGLV GEIISRFEKK GFKLIGLKMF 130 140 150 160 170 180 QCPKELAEEH YKDLSAKSFF PNLIEYITSG PVVCMAWEGV GVVASARKLI GKTDPLQAEP 190 200 210 220 230 GTIRGDLAVQ TGRNIVHGSD SPENGKREIG LWFKEGELCK WDSALATWLR E

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of nucleoside diphosphate kinase 2 from Arabidopsis thaliana." Yi H., Song P.-S., Choi G. Plant Gene Register PGR98-056 Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Columbia.
[2]	"UV responsive genes of Arabidopsis revealed by similarity to the Gcn4 mediated UV response in yeast." Zimmermann S., Baumann A., Jaekel K., Marbach I., Engelberg D., Frohnmeyer H. J. Biol. Chem. 274:17017-17024(1999) [PubMed: 10358052] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Landsberg erecta.
[3]	"Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones." Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N., Tabata S. DNA Res. 4:401-414(1997) [PubMed: 9501997] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	"Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones." Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H., Tabata S. DNA Res. 7:31-63(2000) [PubMed: 10718197] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[5]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[6]	"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: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[7]	"NDP kinase 2 interacts with two oxidative stress-activated MAPKs to regulate cellular redox state and enhances multiple stress tolerance in transgenic plants." Moon H., Lee B., Choi G., Shin D., Prasad D.T., Lee O., Kwak S.-S., Kim D.H., Nam J., Bahk J., Hong J.C., Lee S.Y., Cho M.J., Lim C.O., Yun D.-J. Proc. Natl. Acad. Sci. U.S.A. 100:358-363(2003) [PubMed: 12506203] [Abstract] Cited for: FUNCTION, INDUCTION, PHOSPHORYLATION, INTERACTION WITH MPK3 AND MPK6.
[8]	"The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts." Peltier J.-B., Cai Y., Sun Q., Zabrouskov V., Giacomelli L., Rudella A., Ytterberg A.J., Rutschow H., van Wijk K.J. Mol. Cell. Proteomics 5:114-133(2006) [PubMed: 16207701] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY.
[9]	"Sorting signals, N-terminal modifications and abundance of the chloroplast proteome." Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q., van Wijk K.J. PLoS ONE 3:E1994-E1994(2008) [PubMed: 18431481] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY.
[10]	"Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks." Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S. Plant Physiol. 150:889-903(2009) [PubMed: 19376835] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201, MASS SPECTROMETRY. Strain: cv. Columbia. Tissue: Seedling.
[11]	"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: 15465053] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 79-231 IN COMPLEX WITH ATP ANALOG, INTERACTION WITH PHYA.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00517103.

PIR

T51612.
T52586.

RefSeq

NP_568970.2. NM_125726.3.

UniGene

At.24504.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1S57	X-ray	1.80	A/B/C/D/E/F	79-231	[»]
1S59	X-ray	2.60	A/B/C/D/E/F	79-231	[»]

ProteinModelPortal

O64903.

SMR

O64903. Positions 79-231.

ModBase

Search...

Protein-protein interaction databases

IntAct

O64903. 15 interactions.

STRING

O64903.

Proteomic databases

PRIDE

O64903.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT5G63310.1; AT5G63310.1; AT5G63310.

GeneID

836451.

GenomeReviews

Gene locus AT5G63310 in contig BA000015_GR.

KEGG

ath:AT5G63310.

Organism-specific databases

TAIR

At5g63310.

Phylogenomic databases

HOGENOM

HBG445152.

InParanoid

O64903.

OMA

QLFFAPQ.

PhylomeDB

O64903.

ProtClustDB

CLSN2722776.

Enzyme and pathway databases

BioCyc

ARA:AT5G63310-MONOMER.

Gene expression databases

ArrayExpress

O64903.

Genevestigator

O64903.

GermOnline

AT5G63310. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]

Gene3D

G3DSA:3.30.70.141. NDK. 1 hit.

KO

K00940.

PANTHER

PTHR11349. Nuc_diP_kinase_core. 1 hit.

Pfam

PF00334. NDK. 1 hit.
[Graphical view]

PRINTS

PR01243. NUCDPKINASE.

SMART

SM00562. NDK. 1 hit.
[Graphical view]

SUPFAM

SSF54919. NDK. 1 hit.

PROSITE

PS00469. NDP_KINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

NDK2_ARATH

Accession

Primary (citable) accession number: O64903
Secondary accession number(s): O65212, Q9SMX6

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 1998
Last sequence update:	January 11, 2001
Last modified:	December 14, 2011
This is version 103 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program