Reviewed, UniProtKB/Swiss-Prot P39207 (NDK1_ARATH)

Names and origin

Protein names

Recommended name:
    Nucleoside diphosphate kinase 1
    EC=2.7.4.6
Alternative name(s):
    Nucleoside diphosphate kinase I
      Short name=NDP kinase I
      Short name=NDPK I
      Short name=NDK I

Gene names

Name:	NDPK1
Ordered Locus Names:	At4g09320
ORF Names:	T30A10.80

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	149 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.
Catalytic activity	ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
Cofactor	Magnesium By similarity.
Sequence similarities	Belongs to the NDK family.
Sequence caution	The sequence CAA49173.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Nucleotide metabolism
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete 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 response to cadmium ion Inferred from expression pattern. Source: TAIR response to salt stress Inferred from expression pattern. Source: TAIR
Cellular component	apoplast Inferred from direct assay. Source: TAIR chloroplast Inferred from direct assay. Source: TAIR peroxisome Inferred from direct assay. Source: TAIR plasma membrane Inferred from direct assay. Source: TAIR vacuole Inferred from direct assay. Source: TAIR
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside diphosphate kinase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 149

149

Nucleoside diphosphate kinase 1

PRO_0000137134

Sites

Active site

115

1

Pros-phosphohistidine intermediate By similarity

Binding site

9

1

ATP By similarity

Binding site

57

1

ATP By similarity

Binding site

85

1

ATP By similarity

Binding site

91

1

ATP By similarity

Binding site

102

1

ATP By similarity

Binding site

112

1

ATP By similarity

Experimental info

Sequence conflict

30 – 31

2

FT → LH in CAA79265. Ref.4

Secondary structure

1

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149

Helix Strand Turn

Details...

Beta strand

3 – 8

6

Helix

10 – 14

5

Helix

18 – 28

11

Beta strand

31 – 38

8

Helix

42 – 48

7

Beta strand

53 – 55

3

Helix

58 – 65

8

Beta strand

70 – 77

8

Helix

80 – 88

9

Turn

93 – 95

3

Helix

101 – 105

5

Beta strand

113 – 116

4

Helix

120 – 130

11

Helix

143 – 145

3

Sequences

	Sequence		Length	Mass (Da)
	P39207-1 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: 21DF53932A07B0BA	FASTA	149	16,500
	10 20 30 40 50 60 MEQTFIMIKP DGVQRGLIGE VICRFEKKGF TLKGLKLISV ERSFAEKHYE DLSSKSFFSG 70 80 90 100 110 120 LVDYIVSGPV VAMIWEGKNV VLTGRKIIGA TNPAASEPGT IRGDFAIDIG RNVIHGSDSV 130 140 ESARKEIALW FPDGPVNWQS SVHPWVYET

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 10617198] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	"An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana." Hoefte H., Desprez T., Amselem J., Chiapello H., Rouze P., Caboche M., Moisan A., Jourjon M.-F., Charpenteau J.-L., Berthomieu P., Guerrier D., Giraudat J., Quigley F., Thomas F., Yu D.-Y., Mache R., Raynal M., Cooke R. , Grellet F., Delseny M., Parmentier Y., de Marcillac G., Gigot C., Fleck J., Philipps G., Axelos M., Bardet C., Tremousaygue D., Lescure B. Plant J. 4:1051-1061(1993) [PubMed: 8281187] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 5-81. Strain: cv. Columbia. Tissue: Flower.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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.
Z18791 mRNA. Translation: CAA79265.1.

IPI

IPI00521214.

PIR

S31444.
S31446.
T17131.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1U8W	X-ray	2.40	A/B/C/D/E/F	1-149	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

P39207.

2-D gel databases

SWISS-2DPAGE

P39207.

Proteomic databases

PRIDE

P39207.

Genome annotation databases

GenomeReviews

Gene locus AT4G09320 in contig CT486007_GR.

Organism-specific databases

TAIR

At4g09320.

Enzyme and pathway databases

BRENDA

2.7.4.6. 302.

Gene expression databases

ArrayExpress

P39207.

Genevestigator

P39207.

GermOnline

AT4G09320. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR001564. Nuc_diP_kinase_core.
[Graphical view]

Gene3D

G3DSA:3.30.70.141. NDK. 1 hit.

PANTHER

PTHR11349. Nuc_diP_kinase_core. 1 hit.

Pfam

PF00334. NDK. 1 hit.
[Graphical view]

PRINTS

PR01243. NUCDPKINASE.

ProDom

PD001018. NDK. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00562. NDK. 1 hit.
[Graphical view]

PROSITE

PS00469. NDP_KINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

NDK1_ARATH

Accession

Primary (citable) accession number: P39207
Secondary accession number(s): Q41989

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	November 3, 2009
This is version 82 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)