Detailed view for TcCLB.504005.10

Basic information

TDR Targets ID: 42034
Trypanosoma cruzi, endonuclease III, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.7769 | Length (AA): 251 | MW (Da): 28213 | Paralog Number: 1

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

Druggability Group : DG3

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

PF00633   Helix-hairpin-helix motif
PF00730   HhH-GPD superfamily base excision DNA repair protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0003906   DNA-(apurinic or apyrimidinic site) lyase activity  
GO:0051539   4 iron, 4 sulfur cluster binding  
GO:0019104   DNA N-glycosylase activity  
GO:0006285   base-excision repair, AP site formation  
GO:0005634   nucleus  
GO:0004519   endonuclease activity  
GO:0003824   catalytic activity  
GO:0003677   DNA binding  
GO:0006281   DNA repair  
GO:0006284   base-excision repair  

Metabolic Pathways

Base excision repair (KEGG)

Structural information

Modbase 3D models:

There are 6 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
20 247 1kg2 (A) 4 224 22.00 0 1 1.2 -0.76
23 235 1orn (A) 4 214 26.00 0 1 1.32 -1.23
3 243 3n5n (X) 70 304 20.00 0 1 1.22996 -0.54
11 227 2abk (A) 2 204 31.00 0 1 1.27734 -0.95
20 235 1orn (A) 5 214 26.00 0 1 1.28036 -1.12
21 231 1kea (A) 7 218 23.00 0 1 1.21744 -0.66

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_126913)

Species Accession Gene Product
Arabidopsis thaliana AT1G05900   endonuclease III 2
Arabidopsis thaliana AT2G31450   protein NTH1
Babesia bovis BBOV_I003140   base excision DNA repair protein, HhH-GPD family domain containing protein
Brugia malayi Bm1_27990   Endonuclease III-like protein 1
Candida albicans CaO19.12564   similar to S. cerevisiae NTG1 (YAL015C) endonuclease III-like glycosylase involved in DNA repair
Candida albicans CaO19.5098   similar to S. cerevisiae NTG1 (YAL015C) endonuclease III-like glycosylase involved in DNA repair
Caenorhabditis elegans CELE_R10E4.5   Protein NTH-1, isoform C
Cryptosporidium hominis Chro.70202   endonuclease III
Cryptosporidium parvum cgd7_1720   endonuclease III, putative
Chlamydia trachomatis CT_697   endonuclease III
Dictyostelium discoideum DDB_G0277247   hypothetical protein
Drosophila melanogaster Dmel_CG9272   CG9272 gene product from transcript CG9272-RA
Escherichia coli b1633   DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)
Echinococcus granulosus EgrG_001090300   endonuclease III protein 1
Entamoeba histolytica EHI_083460   endonuclease III, putative
Echinococcus multilocularis EmuJ_001090300   endonuclease III protein 1
Giardia lamblia GL50803_3595   Endonuclease III
Homo sapiens ENSG00000065057   nth endonuclease III-like 1 (E. coli)
Leishmania braziliensis LbrM.09.0070   endonuclease III, putative
Leishmania donovani LdBPK_090070.1   endonuclease III, putative
Leishmania infantum LinJ.09.0070   endonuclease III, putative
Leishmania major LmjF.09.0050   endonuclease III, putative
Leishmania mexicana LmxM.09.0050   endonuclease III, putative
Loa Loa (eye worm) LOAG_15925   hypothetical protein
Loa Loa (eye worm) LOAG_03833   hypothetical protein
Loa Loa (eye worm) LOAG_10605   hypothetical protein
Mycobacterium leprae ML2301c   PROBABLE ENDONUCLEASE III NTH (DNA-(APURINIC OR APYRIMIDINIC SITE)LYASE) (AP LYASE) (AP ENDONUCLEASE CLASS I) (ENDODEOXYRIBONUCL
Mus musculus ENSMUSG00000041429   nth (endonuclease III)-like 1 (E.coli)
Mycobacterium tuberculosis Rv3674c   Probable endonuclease III Nth (DNA-(apurinic or apyrimidinic site)lyase) (AP lyase) (AP endonuclease class I) (endodeoxyribonucl
Mycobacterium ulcerans MUL_4248   endonuclease III Nth
Neospora caninum NCLIV_070230   hypothetical protein
Oryza sativa 9268162   Os11g0267300
Onchocerca volvulus OVOC3819   Endonuclease III homolog
Plasmodium berghei PBANKA_1229500   endonuclease III homologue, putative
Plasmodium falciparum PF3D7_0614800   endonuclease III homologue, putative
Plasmodium knowlesi PKNH_1135200   endonuclease III homologue, putative
Plasmodium vivax PVX_113875   endonuclease III homologue, putative
Plasmodium yoelii PY05677   Drosophila melanogaster CG9272 gene product
Saccharomyces cerevisiae YOL043C   bifunctional N-glycosylase/AP lyase NTG2
Saccharomyces cerevisiae YAL015C   bifunctional N-glycosylase/AP lyase NTG1
Schistosoma japonicum Sjp_0205880   ko:K01741 DNA-(apurinic or apyrimidinic site) lyase [EC4.2.99.18], putative
Schistosoma mansoni Smp_006710   endonuclease III
Schmidtea mediterranea mk4.044559.03   Endonuclease III homolog
Schmidtea mediterranea mk4.052422.00   Endonuclease III homolog
Schmidtea mediterranea mk4.007699.01   Endonuclease III homolog
Trypanosoma brucei gambiense Tbg972.11.13530   endonuclease III, putative
Trypanosoma brucei Tb927.11.12090   endonuclease III, putative
Trypanosoma congolense TcIL3000.11.12720   endonuclease III, putative
Trypanosoma cruzi TcCLB.504005.10   endonuclease III, putative
Trypanosoma cruzi TcCLB.511481.50   endonuclease III, putative
Toxoplasma gondii TGME49_305920   endonuclease III family 1 protein
Treponema pallidum TP0775   endonuclease III (nth)
Theileria parva TP03_0162   endonuclease III, putative
Trichomonas vaginalis TVAG_113220   endonuclease III, putative
Trichomonas vaginalis TVAG_447840   endonuclease III, putative
Wolbachia endosymbiont of Brugia malayi Wbm0365   EndoIII-related endonuclease

Essentiality

TcCLB.504005.10 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.3910 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.3910 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.3910 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.3910 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b1633 Escherichia coli non-essential goodall
TGME49_305920 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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 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

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.504005.10 (Trypanosoma cruzi), endonuclease III, putative
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