Detailed view for Rv0491

Basic information

TDR Targets ID: 6996
Mycobacterium tuberculosis, Two component sensory transduction protein RegX3 (transcriptional regulatory protein) (probably LuxR-family)
Source Database / ID:  Tuberculist 

pI: 4.5809 | Length (AA): 227 | MW (Da): 24849 | 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

PF00072   Response regulator receiver domain
PF00486   Transcriptional regulatory protein, C terminal

Gene Ontology

Mouse over links to read term descriptions.
GO:0000160   two-component signal transduction system (phosphorelay)  
GO:0006355   regulation of transcription, DNA-dependent  
GO:0003677   DNA binding  
GO:0000156   two-component response regulator activity  

Metabolic Pathways

Two-component system (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
2 226 2oqr (A) 2 226 99.99 0 1 2.15509 -0.77
3 39 4l4u (A) 2 38 24.00 0 0.59 0.395196 0.43
127 226 2d1v (A) 131 230 45.00 0 1 1.16873 -2.02

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:

PDB tag
  • 2GWR:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2OQR:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3R0J:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5ED4:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Dormant phase. murphy
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_131511)

Species Accession Gene Product
Escherichia coli b3912   response regulator in two-component regulatory system with CpxA
Escherichia coli b0399   response regulator in two-component regulatory system with PhoR (or CreC)
Mycobacterium leprae ML2439c   TWO COMPONENT SENSORY TRANSDUCTION PROTEIN REGX3 (TRANSCRIPTIONAL REGULATORY PROTEIN) (PROBABLY LUXR-FAMILY)
Mycobacterium leprae ML0773   probable two-component sensory transduction transcriptional regulatory protein MtrA
Mycobacterium tuberculosis Rv0491   Two component sensory transduction protein RegX3 (transcriptional regulatory protein) (probably LuxR-family)
Mycobacterium ulcerans MUL_1501   two component regulator receiver domain-containing protein
Mycobacterium ulcerans MUL_4560   two component sensory transduction protein RegX3
Schmidtea mediterranea mk4.071585.02  

Essentiality

Rv0491 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu496 this record Mycobacterium tuberculosis non-essential nmpdr
b0399 Escherichia coli non-essential goodall
b3912 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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

Druggability index (range: 0 to 1): 0.2

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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User comments

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Gene identifier Rv0491 (Mycobacterium tuberculosis), Two component sensory transduction protein RegX3 (transcriptional regulatory protein) (probably LuxR-family)
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