A2BU01 (NDK_PROM5) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Nucleoside diphosphate kinase
Short name=NDK
Short name=NDP kinase
EC=2.7.4.6

Alternative name(s):
Nucleoside-2-P kinase

Gene names

Name:	ndk
Ordered Locus Names:	P9515_00531

Organism

Prochlorococcus marinus (strain MIT 9515) [Complete proteome] [HAMAP]

Taxonomic identifier

167542 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Cyanobacteria › Prochlorales › Prochlorococcaceae › Prochlorococcus › Prochlorococcus marinus

Protein attributes

Sequence length	152 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

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 By similarity. HAMAP-Rule MF_00451
Catalytic activity	ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. HAMAP-Rule MF_00451
Cofactor	Magnesium By similarity.
Subunit structure	Homotetramer By similarity.
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Belongs to the NDK family.

Ontologies

Keywords
Biological process	Nucleotide metabolism
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	CTP biosynthetic process Inferred from electronic annotation. Source: HAMAP GTP biosynthetic process Inferred from electronic annotation. Source: HAMAP UTP biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside diphosphate kinase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 152	152	Nucleoside diphosphate kinase HAMAP-Rule MF_00451		PRO_1000026272
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)
	A2BU01 [UniParc]. Last modified February 20, 2007. Version 1. Checksum: D42E99B1DF7F2831	FASTA	152	17,194
	10 20 30 40 50 60 MIKERTFLAI KPDGVQRGYI AEIIGRFEKK GFKLVGLKQL IPSKQLAQDH YGVHRERPFF 70 80 90 100 110 120 KDLVNFISSG PVVAMIWEGE GVILSARKII GATKPLEAEP GTIRGDLAID IGRNIIHGSD 130 140 150 GEETAKFEIN LWFDQHEICD WETSDSEWRV ES

References

[1]

"Patterns and implications of gene gain and loss in the evolution of Prochlorococcus." Kettler G.C., Martiny A.C., Huang K., Zucker J., Coleman M.L., Rodrigue S., Chen F., Lapidus A., Ferriera S., Johnson J., Steglich C., Church G.M., Richardson P., Chisholm S.W. PLoS Genet. 3:2515-2528(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: MIT 9515.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000552 Genomic DNA. Translation: ABM71262.1.
RefSeq	YP_001010369.1. NC_008817.1.
3D structure databases
ProteinModelPortal	A2BU01.
SMR	A2BU01. Positions 4-148.
ModBase	Search...
Protein-protein interaction databases
STRING	167542.P9515_00531.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ABM71262; ABM71262; P9515_00531.
GeneID	4719929.
KEGG	pmc:P9515_00531.
PATRIC	23013620. VBIProMar113831_0055.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0105.
HOGENOM	HOG000224564.
KO	K00940.
OMA	FRVVAMK.
ProtClustDB	PRK00668.
Enzyme and pathway databases
BioCyc	PMAR167542:GI3N-96-MONOMER.
Family and domain databases
Gene3D	3.30.70.141. 1 hit.
HAMAP	MF_00451. NDP_kinase.
InterPro	IPR001564. Nucleoside_diP_kinase. IPR023005. Nucleoside_diP_kinase_AS. [Graphical view]
PANTHER	PTHR11349. PTHR11349. 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

NDK_PROM5

Accession

Primary (citable) accession number: A2BU01

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	February 20, 2007
Last modified:	May 1, 2013
This is version 46 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program