Detailed view for Rv0670

Basic information

TDR Targets ID: 981052
Mycobacterium tuberculosis, Probable endonuclease IV End (endodeoxyribonuclease IV) (apurinase)
Source Database / ID:  Tuberculist 

pI: 5.3275 | Length (AA): 252 | MW (Da): 26813 | 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

PF01261  

Gene Ontology

Mouse over links to read term descriptions.
GO:0008270   zinc ion binding  
GO:0003677   DNA binding  
GO:0006281   DNA repair  

Metabolic Pathways

Base excision repair (KEGG)

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
1 252 5zhz (A) 1 252 99.99 0 1 2.2574 -1.65

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_129467)

Species Accession Gene Product
Babesia bovis BBOV_III005900   apurinic endonuclease (APN1) family protein
Brugia malayi Bm1_22525   DNA-(Apurinic or apyrimidinic site) lyase
Candida albicans CaO19.7428   apurinic/apyrimidinic endonuclease/3'-repair diesterase
Caenorhabditis elegans CELE_T05H10.2   Protein APN-1
Cryptosporidium hominis Chro.10041   apurinic/apyrimidinic endonuclease Apn1
Cryptosporidium parvum cgd1_310   AP endonuclease of the TIM barrel fold, possible bacterial horizontal transfer
Chlamydia trachomatis CT_625   endonuclease IV
Dictyostelium discoideum DDB_G0279923   apurinic/apyrimidinic endonuclease
Escherichia coli b2159   endonuclease IV with intrinsic 3'-5' exonuclease activity
Loa Loa (eye worm) LOAG_10727   hypothetical protein
Mycobacterium leprae ML1889c   PROBABLE ENDONUCLEASE IV END (ENDODEOXYRIBONUCLEASE IV) (APURINASE)
Mycobacterium tuberculosis Rv0670   Probable endonuclease IV End (endodeoxyribonuclease IV) (apurinase)
Mycobacterium ulcerans MUL_0751   endonuclease IV
Neospora caninum NCLIV_041140   endonuclease V, putative
Plasmodium berghei PBANKA_1347400   apurinic/apyrimidinic endonuclease Apn1, putative
Plasmodium falciparum PF3D7_1332600   apurinic/apyrimidinic endonuclease Apn1, putative
Plasmodium knowlesi PKNH_1268000   apurinic/apyrimidinic endonuclease Apn1, putative
Plasmodium vivax PVX_082560   apurinic/apyrimidinic endonuclease Apn1, putative
Plasmodium yoelii PY05725   AP endonuclease 1
Saccharomyces cerevisiae YKL114C   DNA-(apurinic or apyrimidinic site) lyase APN1
Schmidtea mediterranea mk4.018963.01   DNA-(apurinic or apyrimidinic site) lyase
Schmidtea mediterranea mk4.018963.02  
Schmidtea mediterranea mk4.027782.00  
Toxoplasma gondii TGME49_288680   endonuclease IV APN
Theileria parva TP02_0334   apurinic/apyrimidinic endonuclease, putative

Essentiality

Rv0670 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b2159 Escherichia coli non-essential goodall
CELE_T05H10.2 Caenorhabditis elegans embryonic lethal wormbase
TGME49_288680 Toxoplasma gondii Probably non-essential sidik
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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.

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
Species Known druggable target Linked compounds Reference
Escherichia coli endonuclease IV with intrinsic 3'-5' exonuclease activity 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
0.0081 0.3105 1
0.0086 0.2841 0.661
0.0093 0.2796 1
0.0081 0.4086 1
0.0172 0.3245 1
0.0093 0.2752 0.5845
0.0078 0.2797 0.5822
0.0093 0.358 0.3522
0.0093 0.2916 1
0.0064 0.2796 1
0.0093 0.2857 1
0.0079 0.2897 0.6285
0.0092 0.3105 0.2692
0.0091 0.2824 1
0.0065 0.2752 0.5845
0.0066 0.4223 1
0.0053 0.3167 1
0.0164 0.3194 1
0.0077 0.3219 0.4565
0.0055 0.3439 1
0.0091 0.2821 1
0.017 0.3156 1
0.0152 0.3212 1
0.0084 0.3111 1
0.0076 0.2806 1
0.0074 0.2797 1
0.008 0.2733 0.5822
0.0075 0.2607 0.5664
0.0076 0.2795 0.5822
0.0082 0.3174 0.3154
0.0093 0.2859 1
0.0075 0.3066 1
0.0093 0.306 0.3946
0.0093 0.4225 1
0.0093 0.3793 1
0.0077 1 1
0.008 0.2733 0.5822
0.0092 0.3105 0.2692
0.0116 0.3711 1
0.0079 0.2733 0.5822
0.0076 0.2975 1
0.0116 0.3721 1
0.0093 0.3111 1
0.0079 0.2733 0.5822
0.0091 0.2821 1
0.015 0.3307 1
0.0061 0.2975 0.5822
0.0062 0.2916 1
0.0085 0.4223 1
0.017 0.3156 1
0.0075 0.2733 0.5822
0.0068 0.3111 0.2738
0.0079 0.2733 0.5822
0.0092 0.4932 0.5822
0.0086 0.4794 0.5822
0.0075 0.2607 0.5664
0.0093 0.2752 0.5845
0.0152 0.3254 1
0.0081 0.4086 1
0.0091 0.2515 1
0.0152 0.3229 1
0.008 0.423 0.6114
0.008 0.2733 0.5822
0.0085 1 1
0.0166 0.3224 1
0.0079 0.2733 0.5822
0.0078 0.3105 1
0.0093 0.2975 1
0.0081 0.2664 1
0.0092 0.3105 0.2692

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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User comments

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Gene identifier Rv0670 (Mycobacterium tuberculosis), Probable endonuclease IV End (endodeoxyribonuclease IV) (apurinase)
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