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Protein

Nucleoside diphosphate kinase

Gene

ndk

Organism
Geobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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.UniRule annotation

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.UniRule annotation

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei9 – 91ATPUniRule annotation
Binding sitei57 – 571ATPUniRule annotation
Binding sitei85 – 851ATPUniRule annotation
Binding sitei91 – 911ATPUniRule annotation
Binding sitei102 – 1021ATPUniRule annotation
Binding sitei112 – 1121ATPUniRule annotation
Active sitei115 – 1151Pros-phosphohistidine intermediateUniRule annotation

GO - Molecular functioni

GO - Biological processi

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

BioCyciGBEM404380:GHFR-1698-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinaseUniRule annotation (EC:2.7.4.6UniRule annotation)
Short name:
NDKUniRule annotation
Short name:
NDP kinaseUniRule annotation
Alternative name(s):
Nucleoside-2-P kinaseUniRule annotation
Gene namesi
Name:ndkUniRule annotation
Ordered Locus Names:Gbem_1654
OrganismiGeobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622)
Taxonomic identifieri404380 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfuromonadalesGeobacteraceaeGeobacter
Proteomesi
  • UP000008825 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 137137Nucleoside diphosphate kinasePRO_1000192255Add
BLAST

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Homotetramer.UniRule annotation

Protein-protein interaction databases

STRINGi404380.Gbem_1654.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
HOGENOMiHOG000224565.
KOiK00940.
OMAiAEHSERP.
OrthoDBiEOG67DPRV.

Family and domain databases

HAMAPiMF_00451. NDP_kinase.
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.

B5E9D0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MERTFAIIKP DAVERNVTGK VLAMIEEGGF KIVGMKKIRL SKCQAEGFYY
60 70 80 90 100
VHKERPFFGD LCAFMSRGPV IALVLEKENA IADWRGLMGA TNPANAEAGT
110 120 130
IRKALGVSIE ENTVHGSDSP ESASYEIPYF FNQLELV
Length:137
Mass (Da):15,145
Last modified:October 14, 2008 - v1
Checksum:i44B7B7677850FE7C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001124 Genomic DNA. Translation: ACH38672.1.
RefSeqiWP_012530089.1. NC_011146.1.

Genome annotation databases

EnsemblBacteriaiACH38672; ACH38672; Gbem_1654.
KEGGigbm:Gbem_1654.
PATRICi21987038. VBIGeoBem56306_1646.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001124 Genomic DNA. Translation: ACH38672.1.
RefSeqiWP_012530089.1. NC_011146.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi404380.Gbem_1654.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACH38672; ACH38672; Gbem_1654.
KEGGigbm:Gbem_1654.
PATRICi21987038. VBIGeoBem56306_1646.

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
HOGENOMiHOG000224565.
KOiK00940.
OMAiAEHSERP.
OrthoDBiEOG67DPRV.

Enzyme and pathway databases

BioCyciGBEM404380:GHFR-1698-MONOMER.

Family and domain databases

HAMAPiMF_00451. NDP_kinase.
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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bem / ATCC BAA-1014 / DSM 16622.

Entry informationi

Entry nameiNDK_GEOBB
AccessioniPrimary (citable) accession number: B5E9D0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: October 14, 2008
Last modified: November 11, 2015
This is version 47 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.