Detailed view for TcCLB.511191.10

Basic information

TDR Targets ID: 39191
Trypanosoma cruzi, tyrosyl-DNA Phosphodiesterase (Tdp1), putative

Source Database / ID:  TriTrypDB  GeneDB

pI: 8.513 | Length (AA): 551 | MW (Da): 63168 | Paralog Number: 1

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

Pfam domains

PF06087   Tyrosyl-DNA phosphodiesterase

Gene Ontology

Mouse over links to read term descriptions.
GO:0005634   nucleus  
GO:0008081   phosphoric diester hydrolase activity  
GO:0006281   DNA repair  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 3 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
8 512 1jy1 (A) 166 602 34.00 0 1 1.09 -0.27
1 515 1jy1 (A) 158 605 32.00 0 1 1.07656 0.1
7 513 1rff (A) 165 603 34.00 0 1 1.06555 0.29

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 metacyclic. Smircich P
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile epimastigote. Smircich P
Show/Hide expression data references
  • Smircich P Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi.

Orthologs

Ortholog group members (OG5_129037)

Species Accession Gene Product
Arabidopsis thaliana AT5G15170   tyrosyl-DNA phosphodiesterase 1
Brugia malayi Bm1_36420   Tyrosyl-DNA phosphodiesterase family protein
Caenorhabditis elegans CELE_F52C12.1   Protein F52C12.1
Cryptosporidium hominis Chro.70273   hypothetical protein
Cryptosporidium parvum cgd7_2390   tyrosyl-DNA phodphodiesterase 1 (tdp1)
Drosophila melanogaster Dmel_CG8825   glaikit
Echinococcus granulosus EgrG_000433000   transcription factor Dp 1
Echinococcus granulosus EgrG_000433100   tyrosyl DNA phosphodiesterase 1
Entamoeba histolytica EHI_148390   tyrosyl-DNA phosphodiesterase, putative
Echinococcus multilocularis EmuJ_000433000   transcription factor Dp 1
Echinococcus multilocularis EmuJ_000433100   tyrosyl DNA phosphodiesterase 1
Homo sapiens ENSG00000042088   tyrosyl-DNA phosphodiesterase 1
Leishmania braziliensis LbrM.33.3330   tyrosyl-DNA phosphodiesterase, putative;with=GeneDB:LinJ33_V3.3210
Leishmania donovani LdBPK_333210.1   tyrosyl-DNA phosphodiesterase-like protein
Leishmania infantum LinJ.33.3210   tyrosyl-DNA phosphodiesterase 1
Leishmania major LmjF.33.3050   tyrosyl-DNA phosphodiesterase 1
Leishmania mexicana LmxM.32.3050   tyrosyl-DNA phosphodiesterase-like protein
Loa Loa (eye worm) LOAG_02315   tyrosyl-DNA phosphodiesterase
Mus musculus ENSMUSG00000021177   tyrosyl-DNA phosphodiesterase 1
Oryza sativa 4343446   Os07g0530100
Saccharomyces cerevisiae YBR223C   tyrosyl-DNA phosphodiesterase 1
Schistosoma japonicum Sjp_0012210   ko:K01113 phosphodiesterase/alkaline phosphatase D [EC3.1.4.1], putative
Schistosoma mansoni Smp_129800   tyrosyl-DNA phosphodiesterase
Schmidtea mediterranea mk4.008114.01  
Schmidtea mediterranea mk4.006310.01  
Schmidtea mediterranea mk4.024191.00   Probable tyrosyl-DNA phosphodiesterase
Schmidtea mediterranea mk4.006310.00   Tyrosyl-DNA phosphodiesterase 1
Schmidtea mediterranea mk4.002468.00   E2F dimerization protein
Trypanosoma brucei gambiense Tbg.972.2.4040   tyrosyl-DNA Phosphodiesterase (Tdp1), putative
Trypanosoma brucei Tb927.2.5750   tyrosyl-DNA Phosphodiesterase (Tdp1), putative
Trypanosoma congolense TcIL3000_0_25380   tyrosyl-DNA Phosphodiesterase (Tdp1), putative
Trypanosoma cruzi TcCLB.506619.40   tyrosyl-DNA Phosphodiesterase (Tdp1), putative
Trypanosoma cruzi TcCLB.511191.10 this record   tyrosyl-DNA Phosphodiesterase (Tdp1), putative

Essentiality

TcCLB.511191.10 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.2.5750 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.2.5750 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.2.5750 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.2.5750 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?
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 log in using your TDR Targets username and password and send them to us using the corresponding form in this page (only visible to registered users) or 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
Species Known druggable target Linked compounds Reference
Homo sapiens tyrosyl-DNA phosphodiesterase 1 Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.0071 0.2542 0.5761
0.0078 0.2857 1
0.0569 0.3838 1
0.094 0.3301 1
0.1074 0.8141 1
0.0071 0.4302 0.4147
0.0289 0.4194 0.4194
0.008 0.4082 1
0.008 0.4211 0.6843
0.1025 0.8485 1
0.0076 0.3505 0.5
0.0523 0.3191 1
0.0743 0.2645 1
0.008 0.3013 0.5
0.0439 0.3142 1
0.008 0.3968 1
0.0372 0.2638 1
0.0291 0.4522 0.9773
0.0229 0.2657 1
0.0343 0.9403 0.932
0.0368 0.261 1
0.0072 0.2852 1
0.0068 0.2766 1
0.0396 0.4637 0.5
0.0072 0.3656 1
0.008 0.3226 0.5
0.0128 0.3152 1
0.008 0.5164 0.5
0.008 0.5202 1
0.0072 0.336 1
0.0391 0.3817 1
0.008 0.3873 1
0.0069 0.6462 1
0.0069 0.8775 0.8775
0.1125 0.7577 1
0.0481 0.2501 0.2499
0.0273 0.2908 1
0.1168 0.2606 1
0.041 0.2781 0.6154
0.1381 0.8557 1
0.0142 0.3926 1
0.0715 0.8232 0.5
0.008 0.3746 0.624
0.0661 0.2635 1
0.008 0.3721 1
0.0626 0.4168 1
0.008 0.3286 1
0.0724 0.8596 1
0.112 0.2606 1
0.0129 0.2828 1
0.0261 0.2874 1
0.0324 0.4061 1
0.0417 0.2687 1
0.0361 0.252 1
0.0066 0.3652 1
0.0346 0.3424 0.5
0.1039 0.3223 1
0.0135 0.543 0.7729
0.0074 0.2944 0.5
0.1233 0.2683 1
0.0463 0.2875 0.5
0.0138 0.3585 1
0.0064 0.9308 1
0.0069 0.5202 0.5
0.0074 0.2944 0.5
0.0067 0.2504 0.4481
0.008 0.5226 0.5315
0.008 0.2664 1
0.0569 0.3838 1
0.008 0.3049 0.5
0.0064 0.3123 0.8066
0.1383 0.8724 1
0.0374 0.3754 1
0.0324 0.4061 1
0.0883 0.3102 1
0.0364 0.7819 0.5
0.1026 0.3006 1
0.0077 0.2776 1
0.0138 0.2769 0.3351
0.115 0.7921 1

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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Gene identifier TcCLB.511191.10 (Trypanosoma cruzi), tyrosyl-DNA Phosphodiesterase (Tdp1), putative
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