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Protein

Nucleoside diphosphate kinase

Gene

NDK

Organism
Acanthamoeba polyphaga mimivirus (APMV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays a role in the synthesis of nucleoside triphosphates. This activity may optimize the replication of the AT-rich (73%) viral genome in a thymidine-limited host environment.

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.PROSITE-ProRule annotation

Cofactori

Mg2+By similarity

Kineticsi

KM values are below 10 µM for dCDP, dCTP and dUTP.

  1. KM=140 µM for dGDP1 Publication
  2. KM=41 µM for dGTP1 Publication
  3. KM=5 µM for ADP1 Publication
  4. KM=770 µM for ATP1 Publication
  5. KM=830 µM for GTP1 Publication
  6. KM=100 µM for UDP1 Publication
  7. KM=110 µM for UTP1 Publication
  8. KM=40 µM for CTP1 Publication
  9. KM=50 µM for CDP1 Publication
  10. KM=30 µM for dTTP1 Publication
  11. KM=25 µM for dUTP1 Publication
  1. Vmax=99 µmol/min/mg enzyme toward dGDP1 Publication
  2. Vmax=27 µmol/min/mg enzyme toward dGTP1 Publication
  3. Vmax=50 µmol/min/mg enzyme toward ADP1 Publication
  4. Vmax=140 µmol/min/mg enzyme toward ATP1 Publication
  5. Vmax=450 µmol/min/mg enzyme toward GTP1 Publication
  6. Vmax=110 µmol/min/mg enzyme toward UDP1 Publication
  7. Vmax=41 µmol/min/mg enzyme toward UTP1 Publication
  8. Vmax=25 µmol/min/mg enzyme toward CTP1 Publication
  9. Vmax=70 µmol/min/mg enzyme toward CDP1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei9ATP1
Binding sitei58ATP1
Binding sitei86ATP1
Binding sitei99ATP1
Binding sitei109ATP1
Active sitei112Pros-phosphohistidine intermediatePROSITE-ProRule annotation1

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

BRENDAi2.7.4.6. 9231.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinase (EC:2.7.4.6)
Short name:
NDK
Short name:
NDP kinase
Gene namesi
Name:NDK
Ordered Locus Names:MIMI_R418
OrganismiAcanthamoeba polyphaga mimivirus (APMV)
Taxonomic identifieri212035 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageMimiviridaeMimivirus
Virus hostiAcanthamoeba polyphaga (Amoeba) [TaxID: 5757]
Proteomesi
  • UP000001134 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi62N → L: Increased affinity for NTP and decreased affinity for dNTP. 1 Publication1
Mutagenesisi107R → G: Complete loss of affinity for pyrimidine bases. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001371541 – 137Nucleoside diphosphate kinaseAdd BLAST137

Keywords - PTMi

Phosphoprotein

Structurei

Secondary structure

1137
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 8Combined sources7
Helixi10 – 14Combined sources5
Helixi18 – 27Combined sources10
Beta strandi31 – 40Combined sources10
Helixi43 – 49Combined sources7
Helixi51 – 53Combined sources3
Helixi59 – 66Combined sources8
Beta strandi71 – 78Combined sources8
Helixi81 – 89Combined sources9
Helixi98 – 102Combined sources5
Beta strandi105 – 107Combined sources3
Beta strandi110 – 113Combined sources4
Helixi117 – 127Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2B8PX-ray2.55A/B2-137[»]
2B8QX-ray2.50A/B/C/D/E/F2-137[»]
3B6BX-ray2.00A/B/C/D/E/F2-137[»]
3DDIX-ray1.90A/B2-137[»]
3DKDX-ray1.90A/B2-137[»]
3EE3X-ray2.40A/B/C/D/E/F2-137[»]
3EICX-ray2.30A/B/C/D/E/F2-137[»]
3EJMX-ray1.95A/B2-137[»]
3ELHX-ray2.40A/B/C/D/E/F2-137[»]
3EM1X-ray1.50A/B2-137[»]
3EMTX-ray1.60A/B2-137[»]
3ENAX-ray1.60A/B2-137[»]
3ETMX-ray1.90A/B2-137[»]
3EVMX-ray1.80A/B2-137[»]
3EVOX-ray1.50A/B2-137[»]
3EVWX-ray2.60A/B/C/D/E/F2-137[»]
3FBBX-ray2.40A/B/C/D/E/F2-137[»]
3FBCX-ray2.60A/B/C/D/E/F2-137[»]
3FBEX-ray2.40A/B/C/D/E/F2-137[»]
3FBFX-ray2.60A/B/C/D/E/F2-137[»]
3FC9X-ray2.80A/B/C/D/E/F2-137[»]
3FCVX-ray2.40A/B2-137[»]
3FCWX-ray2.40A/B/C/D/E/F2-137[»]
3G2XX-ray2.70A/B/C/D/E/F2-137[»]
3GP9X-ray1.80A/B/C/D/E/F2-137[»]
3GPAX-ray2.00A/B/C/D/E/F2-137[»]
ProteinModelPortaliQ5UQL3.
SMRiQ5UQL3.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5UQL3.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

KOiK00940.

Family and domain databases

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.

Q5UQL3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQRTLVLIKP DAFERSLVAE IMGRIEKKNF KIVSMKFWSK APRNLIEQHY
60 70 80 90 100
KEHSEQSYFN DNCDFMVSGP IISIVYEGTD AISKIRRLQG NILTPGTIRG
110 120 130
DLANDIRENL IHASDSEDSA VDEISIWFPE TKMETDN
Length:137
Mass (Da):15,750
Last modified:December 7, 2004 - v1
Checksum:i8C1C6C88964D6BBC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY653733 Genomic DNA. Translation: AAV50687.1.
RefSeqiYP_003986922.1. NC_014649.1.

Genome annotation databases

GeneIDi9925039.
KEGGivg:9925039.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY653733 Genomic DNA. Translation: AAV50687.1.
RefSeqiYP_003986922.1. NC_014649.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2B8PX-ray2.55A/B2-137[»]
2B8QX-ray2.50A/B/C/D/E/F2-137[»]
3B6BX-ray2.00A/B/C/D/E/F2-137[»]
3DDIX-ray1.90A/B2-137[»]
3DKDX-ray1.90A/B2-137[»]
3EE3X-ray2.40A/B/C/D/E/F2-137[»]
3EICX-ray2.30A/B/C/D/E/F2-137[»]
3EJMX-ray1.95A/B2-137[»]
3ELHX-ray2.40A/B/C/D/E/F2-137[»]
3EM1X-ray1.50A/B2-137[»]
3EMTX-ray1.60A/B2-137[»]
3ENAX-ray1.60A/B2-137[»]
3ETMX-ray1.90A/B2-137[»]
3EVMX-ray1.80A/B2-137[»]
3EVOX-ray1.50A/B2-137[»]
3EVWX-ray2.60A/B/C/D/E/F2-137[»]
3FBBX-ray2.40A/B/C/D/E/F2-137[»]
3FBCX-ray2.60A/B/C/D/E/F2-137[»]
3FBEX-ray2.40A/B/C/D/E/F2-137[»]
3FBFX-ray2.60A/B/C/D/E/F2-137[»]
3FC9X-ray2.80A/B/C/D/E/F2-137[»]
3FCVX-ray2.40A/B2-137[»]
3FCWX-ray2.40A/B/C/D/E/F2-137[»]
3G2XX-ray2.70A/B/C/D/E/F2-137[»]
3GP9X-ray1.80A/B/C/D/E/F2-137[»]
3GPAX-ray2.00A/B/C/D/E/F2-137[»]
ProteinModelPortaliQ5UQL3.
SMRiQ5UQL3.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi9925039.
KEGGivg:9925039.

Phylogenomic databases

KOiK00940.

Enzyme and pathway databases

BRENDAi2.7.4.6. 9231.

Miscellaneous databases

EvolutionaryTraceiQ5UQL3.

Family and domain databases

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...

Entry informationi

Entry nameiNDK_MIMIV
AccessioniPrimary (citable) accession number: Q5UQL3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 13, 2005
Last sequence update: December 7, 2004
Last modified: November 2, 2016
This is version 73 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.