Detailed view for Rv2593c

Basic information

TDR Targets ID: 7100
Mycobacterium tuberculosis, Probable holliday junction DNA helicase RuvA
Source Database / ID:  Tuberculist 

pI: 6.8842 | Length (AA): 196 | MW (Da): 20189 | Paralog Number: 0

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

PF01330   RuvA N terminal domain
PF07499   RuvA, C-terminal domain
PF14520   Helix-hairpin-helix domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0009379   Holliday junction helicase complex  
GO:0009378   four-way junction helicase activity  
GO:0005524   ATP binding  
GO:0003678   DNA helicase activity  
GO:0003677   DNA binding  
GO:0006310   DNA recombination  
GO:0006281   DNA repair  

Metabolic Pathways

Homologous recombination (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
1 196 1bvs (A) 1 203 81.00 0 1 1.7931 0.39
1 195 2ztd (A) 1 195 99.00 0 1 2.0313 -0.26
147 192 1ixs (A) 145 190 33.00 0 1 0.748494 -1.06

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
  • 1BVS:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2H5X:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2ZTC:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2ZTD:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2ZTE:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 0-20% 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_132770)

Species Accession Gene Product
Chlamydia trachomatis CT_501   Holliday junction ATP-dependent DNA helicase RuvA
Escherichia coli b1861   component of RuvABC resolvasome, regulatory subunit
Mycobacterium leprae ML0482   Probable Holliday junction DNA helicase component RuvA
Mycobacterium tuberculosis Rv2593c   Probable holliday junction DNA helicase RuvA
Mycobacterium ulcerans MUL_1715   Holliday junction DNA helicase RuvA
Schmidtea mediterranea mk4.033874.00  
Treponema pallidum TP0543   Holliday junction DNA helicase (ruvA)
Wolbachia endosymbiont of Brugia malayi Wbm0251   Holliday junction DNA helicase RuvA

Essentiality

Rv2593c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b1861 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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

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
0.0073 0.2991 0.5
0.0072 0.6367 0.5
0.0035 0.6083 0.5
0.0075 0.3839 0.5
0.0069 0.5261 0.5
0.0069 0.5261 0.5
0.0069 0.3677 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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier Rv2593c (Mycobacterium tuberculosis), Probable holliday junction DNA helicase RuvA
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