Detailed view for Rv2986c

Basic information

TDR Targets ID: 6236
Mycobacterium tuberculosis, DNA-binding protein HU homolog HupB (histone-like protein) (HLP) (21-kDa laminin-2-binding protein)
Source Database / ID:  Tuberculist 

pI: 12.4837 | Length (AA): 214 | MW (Da): 22187 | 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

PF00216   Bacterial DNA-binding protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0003677   DNA binding  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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 70 1mul (A) 1 86 39.00 0.00000052 0.81 0.847003 -0.77
1 99 4pt4 (A) 1 99 99.99 0 1 1.59352 -0.39
1 51 1b8z (A) 1 51 41.00 0.000014 1 0.814218 -0.74

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
  • 3C4I:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4DKY:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4PT4:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

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_130206)

Species Accession Gene Product
Babesia bovis BBOV_III002890   conserved hypothetical protein
Chlamydia trachomatis CT_267   DNA-binding protein HU
Escherichia coli b4000   HU, DNA-binding transcriptional regulator, alpha subunit
Escherichia coli b0440   HU, DNA-binding transcriptional regulator, beta subunit
Mycobacterium leprae ML1683c   PROBABLE DNA-BINDING PROTEIN HU HOMOLOG HUPB (HISTONE-LIKE PROTEIN) (HLP) (21-KDA LAMININ-2-BINDING PROTEIN)
Mycobacterium tuberculosis Rv2986c   DNA-binding protein HU homolog HupB (histone-like protein) (HLP) (21-kDa laminin-2-binding protein)
Mycobacterium ulcerans MUL_1970   DNA-binding protein HU HupB-like protein
Neospora caninum NCLIV_045430   DNA-binding protein HU, putative
Toxoplasma gondii TGME49_227970   histone family DNA-binding protein
Treponema pallidum TP0251   DNA-binding protein II
Theileria parva TP04_0110   hypothetical protein, conserved
Trichomonas vaginalis TVAG_243740   DNA-binding protein HU, putative
Wolbachia endosymbiont of Brugia malayi Wbm0572   nucleoid DNA-binding protein

Essentiality

Rv2986c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3036 this record Mycobacterium tuberculosis essential nmpdr
b0440 Escherichia coli non-essential goodall
b4000 Escherichia coli non-essential goodall
TGME49_227970 Toxoplasma gondii Probably essential sidik
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.
  • 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
  • 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

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

  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis HupB binding to fdxA promoter DNA at 500 uM by EMSA

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 Rv2986c (Mycobacterium tuberculosis), DNA-binding protein HU homolog HupB (histone-like protein) (HLP) (21-kDa laminin-2-binding protein)
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