Detailed view for Rv0002

Basic information

TDR Targets ID: 5884
Mycobacterium tuberculosis, DNA polymerase III (beta chain) DnaN (DNA nucleotidyltransferase)
Source Database / ID:  Tuberculist 

pI: 4.5068 | Length (AA): 402 | MW (Da): 42113 | 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

PF00712   DNA polymerase III beta subunit, N-terminal domain
PF02767   DNA polymerase III beta subunit, central domain
PF02768   DNA polymerase III beta subunit, C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0009360   DNA polymerase III complex  
GO:0003677   DNA binding  
GO:0008408   3'-5' exonuclease activity  
GO:0003887   DNA-directed DNA polymerase activity  
GO:0006260   DNA replication  

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
10 402 5agv (A) 10 402 99.99 0 1 2.17861 -1.21
10 402 5agv (A) 10 402 99.99 0 1 2.17861 -1.21
10 402 5agv (A) 10 402 99.99 0 1 2.17861 -1.21

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
  • 3P16:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3RB9:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4TR7:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5AGU:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5AGV:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Lower 20-40% 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_132148)

Species Accession Gene Product
Brugia malayi Bm1_22225   DNA polymerase III, beta subunit
Brugia malayi Bm1_56665   DNA polymerase III, beta subunit
Chlamydia trachomatis CT_075   DNA polymerase III subunit beta
Escherichia coli b3701   DNA polymerase III, beta subunit
Mycobacterium leprae ML0002   Probable DNA polymerase III, [beta] subunit DnaN
Mycobacterium tuberculosis Rv0002   DNA polymerase III (beta chain) DnaN (DNA nucleotidyltransferase)
Mycobacterium ulcerans MUL_0002   DNA polymerase III subunit beta
Treponema pallidum TP0002   DNA polymerase III, subunit beta (dnaN)
Wolbachia endosymbiont of Brugia malayi Wbm0429   DNA polymerase III beta clamp subunit

Essentiality

Rv0002 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b3701 Escherichia coli essential goodall
Show/Hide essentiality data references
  • 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.
  • 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
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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.

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 DNA polymerase III, beta subunit 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
0.0548 0.7332 1
0.1043 0.3148 0.3145
0.0988 1 0.5
0.057 0.5 0.5
0.1044 1 0.5
0.1075 0.6017 0.5
0.057 0.5 0.5
0.0548 0.5 0.5
0.1043 0.3148 0.3145
0.0467 0.5471 1
0.0548 0.7332 1
0.1043 0.3148 0.3145
0.1075 0.6017 0.5
0.0548 0.7332 1
0.0297 0.7844 0.5
0.1043 0.3148 0.3145
0.1043 0.3148 0.3145

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

39 literature references were collected for this gene.

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 Rv0002 (Mycobacterium tuberculosis), DNA polymerase III (beta chain) DnaN (DNA nucleotidyltransferase)
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