P81766 (NDK3_SPIOL) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Nucleoside diphosphate kinase 3 EC=2.7.4.6 Alternative name(s): Nucleoside diphosphate kinase III Short name=NDK III Short name=NDP kinase III Short name=NDPK III
Organism	Spinacia oleracea (Spinach)
Taxonomic identifier	3562 [NCBI]
Taxonomic lineage	Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › Caryophyllales › Amaranthaceae › Spinacia

Protein attributes

Sequence length	153 AA.
Sequence status	Complete.
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. Shows the highest specificity towards GDP.
Catalytic activity	ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
Cofactor	Magnesium By similarity.
Subunit structure	Homohexamer Probable.
Subcellular location	Plastid › chloroplast thylakoid lumen Ref.2 Ref.3.
Sequence similarities	Belongs to the NDK family.
Caution	There are likely two genes encoding for two slightly different proteins, NDK3 and NDK4. The characterization was made on a thylakoid lumen preparation containing probably both proteins.
Biophysicochemical properties	Kinetic parameters: KM=27.4 µM for GDP KM=89.05 µM for ADP pH dependence: Optimum pH is 6.0.

Ontologies

Keywords
Biological process	Nucleotide metabolism
Cellular component	Chloroplast Plastid Thylakoid
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Phosphoprotein
Technical term	Direct protein sequencing
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
Cellular component	chloroplast thylakoid lumen Inferred from electronic annotation. Source: UniProtKB-SubCell
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 electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 153	153	Nucleoside diphosphate kinase 3		PRO_0000137146
Sites
	Active site	117	1	Pros-phosphohistidine intermediate By similarity
	Binding site	11	1	ATP By similarity
	Binding site	59	1	ATP By similarity
	Binding site	87	1	ATP By similarity
	Binding site	93	1	ATP By similarity
	Binding site	104	1	ATP By similarity
	Binding site	114	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	P81766 [UniParc]. Last modified May 30, 2000. Version 1. Checksum: E496E7D51C2B9511	FASTA	153	17,118
	10 20 30 40 50 60 AEFERTFIAI KPDGVQRGLI SEIVARFERK GFSLVAIKVV IPSRPFAQKH YADLKDKPFY 70 80 90 100 110 120 VGLVAYWSSG PVVAMVWEGE GVIKYGRKLI GATDPQKSEP GTIRGDLAVV NGRNIIHGSD 130 140 150 GPETAKDEIK LWFKPEELVN YTHNAEKWIY GDN

References

[1]	"A third type of nucleoside diphosphate kinase from spinach leaves: purification, characterization and amino-acid sequence." Zhang J., Fukui T., Ichikawa A. Biochim. Biophys. Acta 1248:19-26(1995) [PubMed: 7711053] [Abstract] Cited for: PROTEIN SEQUENCE, CHARACTERIZATION. Tissue: Leaf.
[2]	"Multiple evidence for nucleotide metabolism in the chloroplast thylakoid lumen." Spetea C., Hundal T., Lundin B., Heddad M., Adamska I., Andersson B. Proc. Natl. Acad. Sci. U.S.A. 101:1409-1414(2004) [PubMed: 14736920] [Abstract] Cited for: SUBCELLULAR LOCATION, CHARACTERIZATION.
[3]	"Rapid purification of a chloroplast nucleoside diphosphate kinase using CoA-affinity chromatography." Yang L.M., Lamppa G.K. Biochim. Biophys. Acta 1294:99-102(1996) [PubMed: 8645740] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-19, SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
PIR	S60363.
3D structure databases
ProteinModelPortal	P81766.
SMR	P81766. Positions 1-151.
ModBase	Search...
Protein-protein interaction databases
IntAct	P81766. 1 interaction.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
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.
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

NDK3_SPIOL

Accession

Primary (citable) accession number: P81766

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	May 30, 2000
Last modified:	May 31, 2011
This is version 62 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program