Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei9 – 91ATP
Binding sitei58 – 581ATP
Binding sitei86 – 861ATP
Binding sitei99 – 991ATP
Binding sitei109 – 1091ATP
Active sitei112 – 1121Pros-phosphohistidine intermediatePROSITE-ProRule 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

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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi62 – 621N → L: Increased affinity for NTP and decreased affinity for dNTP. 1 Publication
Mutagenesisi107 – 1071R → G: Complete loss of affinity for pyrimidine bases. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 137137Nucleoside diphosphate kinasePRO_0000137154Add
BLAST

Keywords - PTMi

Phosphoprotein

Structurei

Secondary structure

1
137
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 87Combined sources
Helixi10 – 145Combined sources
Helixi18 – 2710Combined sources
Beta strandi31 – 4010Combined sources
Helixi43 – 497Combined sources
Helixi51 – 533Combined sources
Helixi59 – 668Combined sources
Beta strandi71 – 788Combined sources
Helixi81 – 899Combined sources
Helixi98 – 1025Combined sources
Beta strandi105 – 1073Combined sources
Beta strandi110 – 1134Combined sources
Helixi117 – 12711Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-131.
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
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. Positions 1-131.
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: October 14, 2015
This is version 71 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.