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Protein

Nucleoside diphosphate kinase

Gene

ndkA

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Major role in the synthesis of nucleoside triphosphates other than ATP.

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei10 – 101ATPBy similarity
Binding sitei58 – 581ATPBy similarity
Binding sitei86 – 861ATPBy similarity
Binding sitei92 – 921ATPBy similarity
Binding sitei104 – 1041ATPBy similarity
Binding sitei114 – 1141ATPBy similarity
Active sitei117 – 1171Pros-phosphohistidine intermediateBy similarity

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • metal ion binding Source: UniProtKB-KW
  • nuclease activity Source: MTBBASE
  • nucleoside diphosphate kinase activity Source: GO_Central

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

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinase (EC:2.7.4.6)
Short name:
NDK
Short name:
NDKA
Short name:
NDP kinase
Alternative name(s):
Nucleoside-2-P kinase
Gene namesi
Name:ndkA
Synonyms:ndk
Ordered Locus Names:Rv2445c
ORF Names:MTCY428.01, MTV008.01c
OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Taxonomic identifieri83332 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
Proteomesi
  • UP000001584 Componenti: Chromosome

Organism-specific databases

TubercuListiRv2445c.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • extracellular region Source: MTBBASE
  • host cell nucleus Source: MTBBASE
  • intracellular Source: GO_Central
  • plasma membrane Source: MTBBASE
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 136136Nucleoside diphosphate kinasePRO_0000137010Add
BLAST

Proteomic databases

PaxDbiP9WJH7.

Interactioni

Subunit structurei

Homohexamer.1 Publication

Protein-protein interaction databases

STRINGi83332.Rv2445c.

Structurei

Secondary structure

1
136
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 96Combined sources
Helixi11 – 155Combined sources
Helixi19 – 2810Combined sources
Beta strandi32 – 398Combined sources
Helixi43 – 497Combined sources
Helixi51 – 533Combined sources
Beta strandi54 – 563Combined sources
Helixi59 – 668Combined sources
Beta strandi71 – 788Combined sources
Helixi81 – 899Combined sources
Turni94 – 974Combined sources
Helixi103 – 1075Combined sources
Helixi111 – 1133Combined sources
Beta strandi116 – 1183Combined sources
Helixi122 – 13211Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K44X-ray2.60A/B/C/D/E/F1-136[»]
4ANCX-ray2.80A1-136[»]
4ANDX-ray2.81A/B1-136[»]
4ANEX-ray1.90A/B/C/D/E/F1-136[»]
ProteinModelPortaliP9WJH7.
SMRiP9WJH7. Positions 2-136.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
KOiK00940.
OMAiAEHSERP.
PhylomeDBiP9WJH7.

Family and domain databases

HAMAPiMF_00451. NDP_kinase. 1 hit.
InterProiIPR001564. Nucleoside_diP_kinase.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P9WJH7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTERTLVLIK PDGIERQLIG EIISRIERKG LTIAALQLRT VSAELASQHY
60 70 80 90 100
AEHEGKPFFG SLLEFITSGP VVAAIVEGTR AIAAVRQLAG GTDPVQAAAP
110 120 130
GTIRGDFALE TQFNLVHGSD SAESAQREIA LWFPGA
Length:136
Mass (Da):14,508
Last modified:April 16, 2014 - v1
Checksum:iE59E558D514F8CCD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL123456 Genomic DNA. Translation: CCP45238.1.
PIRiC70681.
RefSeqiNP_216961.1. NC_000962.3.
WP_003412592.1. NZ_KK339370.1.

Genome annotation databases

EnsemblBacteriaiCCP45238; CCP45238; Rv2445c.
GeneIDi885905.
KEGGimtu:Rv2445c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL123456 Genomic DNA. Translation: CCP45238.1.
PIRiC70681.
RefSeqiNP_216961.1. NC_000962.3.
WP_003412592.1. NZ_KK339370.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K44X-ray2.60A/B/C/D/E/F1-136[»]
4ANCX-ray2.80A1-136[»]
4ANDX-ray2.81A/B1-136[»]
4ANEX-ray1.90A/B/C/D/E/F1-136[»]
ProteinModelPortaliP9WJH7.
SMRiP9WJH7. Positions 2-136.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi83332.Rv2445c.

Proteomic databases

PaxDbiP9WJH7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCCP45238; CCP45238; Rv2445c.
GeneIDi885905.
KEGGimtu:Rv2445c.

Organism-specific databases

TubercuListiRv2445c.

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
KOiK00940.
OMAiAEHSERP.
PhylomeDBiP9WJH7.

Family and domain databases

HAMAPiMF_00451. NDP_kinase. 1 hit.
InterProiIPR001564. Nucleoside_diP_kinase.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNDK_MYCTU
AccessioniPrimary (citable) accession number: P9WJH7
Secondary accession number(s): L0TCD2, P71904, P84284
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: June 8, 2016
This is version 18 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
    Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.