Detailed view for Rv2924c

Basic information

TDR Targets ID: 6089
Mycobacterium tuberculosis, Probable formamidopyrimidine-DNA glycosylase Fpg (FAPY-DNA glycosylase)
Source Database / ID:  Tuberculist 

pI: 10.3733 | Length (AA): 289 | MW (Da): 31951 | Paralog Number: 1

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

Druggability Group : DG2

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

PF01149   Formamidopyrimidine-DNA glycosylase N-terminal domain
PF06827   Zinc finger found in FPG and IleRS
PF06831   Formamidopyrimidine-DNA glycosylase H2TH domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0003906   DNA-(apurinic or apyrimidinic site) lyase activity  
GO:0016799   hydrolase activity, hydrolyzing N-glycosyl compounds  
GO:0003824   catalytic activity  
GO:0003684   damaged DNA binding  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0008534   oxidized purine base lesion DNA N-glycosylase activity  
GO:0008270   zinc ion binding  
GO:0006284   base-excision repair  
GO:0006281   DNA repair  
GO:0006289   nucleotide-excision repair  

Metabolic Pathways

Base excision repair (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
2 287 1ee8 (A) 1 265 38.00 0 1 1.40382 -0.31
2 289 3twk (A) 2 281 28.00 0 1 1.19074 0.16
2 285 1k82 (A) 1 268 33.00 0 1 1.2627 0.32

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
Mid 40-60% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. hasan
Show/Hide expression data references
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.

Orthologs

Ortholog group members (OG5_130627)

Species Accession Gene Product
Arabidopsis thaliana AT1G52500   formamidopyrimidine-DNA glycosylase
Candida albicans CaO19.10905   similar to plant/bacterial Formamidopyrimidine-DNA glycosylase
Candida albicans CaO19.3402   similar to plant/bacterial Formamidopyrimidine-DNA glycosylase
Escherichia coli b3635   formamidopyrimidine/5-formyluracil/5-hydroxymethyluracil DNA glycosylase
Mycobacterium leprae ML1658c   Probable formamidopyrimidine-DNA glycosylase Fpg (FAPY-DNA GLYCOSYLASE)
Mycobacterium tuberculosis Rv0944   Possible formamidopyrimidine-DNA glycosylase (FAPY-DNA glycosylase)
Mycobacterium tuberculosis Rv2924c   Probable formamidopyrimidine-DNA glycosylase Fpg (FAPY-DNA glycosylase)
Mycobacterium ulcerans MUL_2031   formamidopyrimidine-DNA glycosylase
Mycobacterium ulcerans MUL_4418   formamidopyrimidine-DNA glycosylase
Oryza sativa 4341640   Os06g0643600
Oryza sativa 4345225   Os08g0304900
Wolbachia endosymbiont of Brugia malayi Wbm0589   formamidopyrimidine-DNA glycosylase

Essentiality

Rv2924c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2972 this record Mycobacterium tuberculosis non-essential nmpdr
b3635 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0112 0.4354 1
0.0329 0.8193 1
0.0526 0.7396 1
0.009 0.2627 1
0.0473 0.5497 1
0.0274 0.2558 1
0.0112 0.4262 0.4213
0.0652 0.4573 1
0.0381 0.5134 1
0.0531 0.3275 1
0.0468 0.8555 1
0.0274 0.3128 1
0.0531 0.3275 1
0.0274 0.2998 0.5787
0.0531 0.3275 1
0.0274 0.2998 0.5787
0.0183 0.4879 1
0.009 0.2843 1
0.0531 0.8628 1
0.0307 0.4313 1
0.0285 0.3942 1
0.0112 0.8853 0.5
0.062 0.6741 1
0.018 0.2788 1
0.0274 0.3128 1
0.0389 0.844 1
0.0307 0.4313 1
0.0581 0.574 1
0.0366 0.3573 1
0.0096 0.5453 1
0.0627 0.7485 1
0.0422 0.8518 1
0.052 0.6592 1
0.0376 0.8151 1
0.0112 0.8903 1
0.0092 0.4929 0.5
0.0531 0.3275 1
0.0371 0.4287 1
0.0401 0.4735 1
0.0421 0.3549 0.5
0.0631 0.6542 1
0.0112 0.7092 1
0.0382 0.7182 1
0.0526 0.7396 1
0.0112 0.7472 1
0.0631 0.6542 1
0.0285 0.3942 1
0.0512 0.6511 1
0.009 0.7854 1
0.018 0.2788 1
0.0264 0.2607 1
0.0104 0.8927 1
0.0526 0.7396 1
0.0272 0.8211 1
0.0103 0.654 1
0.0245 0.3087 0.9964
0.0627 0.7485 1
0.0729 0.7708 1
0.0399 0.4481 1
0.0245 0.3087 0.9964
0.0473 0.5497 1
0.0366 0.3573 1
0.0192 0.3131 1
0.0402 0.6954 1
0.018 0.5254 1
0.0396 0.742 1
0.0652 0.4573 1
0.0112 0.2936 0.4051
0.0721 0.6913 1
0.0486 0.3291 1
0.0531 0.3275 1
0.0694 0.667 1
0.009 0.4661 1
0.0721 0.6913 1
0.0274 0.8086 1
0.0526 0.7396 1
0.0568 0.673 1
0.0203 0.4038 1
0.0112 0.3609 0.3637

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 Rv2924c (Mycobacterium tuberculosis), Probable formamidopyrimidine-DNA glycosylase Fpg (FAPY-DNA glycosylase)
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