Detailed view for Tb927.4.1720

Basic information

TDR Targets ID: 16495
Trypanosoma brucei, Nucleoside diphosphate kinase 3
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.1471 | Length (AA): 349 | MW (Da): 38949 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG1

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF00334   Nucleoside diphosphate kinase

Gene Ontology

Mouse over links to read term descriptions.
GO:0005524   ATP binding  
GO:0004550   nucleoside diphosphate kinase activity  
GO:0006241   CTP biosynthetic process  
GO:0006228   UTP biosynthetic process  
GO:0006183   GTP biosynthetic process  

Structural information

Modbase 3D models:

There are 5 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
6 82 2z14 (A) 12 108 25.00 0.000000039 0.98 0.39293 -0.2
203 349 5u2i (A) 1 140 24.00 0 1 0.792503 -0.87
206 348 3ztp (A) 4 142 30.00 0 1 0.886042 -1.02
206 347 1nhk (R) 4 138 30.00 0 1 0.850177 -0.99
208 345 4dut (B) 6 135 35.00 0.00037 1 0.709515 -0.03

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_151263)

Species Accession Gene Product
Leishmania braziliensis LbrM.20.2560   hypothetical protein, conserved
Leishmania donovani LdBPK_342810.1   Nucleoside diphosphate kinase 3
Leishmania infantum LinJ.34.2810   hypothetical protein, conserved
Leishmania major LmjF.34.2980   hypothetical protein, conserved
Leishmania mexicana LmxM.33.2980   hypothetical protein, conserved
Trypanosoma brucei gambiense Tbg972.4.1630   nucleoside diphosphate kinase, putative
Trypanosoma brucei Tb927.4.1720   Nucleoside diphosphate kinase 3
Trypanosoma congolense TcIL3000_4_1360   Nucleoside diphosphate kinase 3
Trypanosoma cruzi TcCLB.510879.210   Nucleoside diphosphate kinase 3

Essentiality

Tb927.4.1720 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.1720 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.1720 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.1720 this record Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.4.1720 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) normal (PATO:0000461) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) increased (PATO:0000470) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant gain of fitness) in procyclic forms . References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

  • Assay for Nucleoside 5'-Diphosphate Kinase (2.7.4.6 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Tb927.4.1720 cloned gene BRENDA A gene with this EC number or name or sequence has been cloned from Trypanosoma brucei ( 1 )

Bibliographic References

3 literature references were collected for this gene.

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Gene identifier Tb927.4.1720 (Trypanosoma brucei), Nucleoside diphosphate kinase 3
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