Detailed view for Rv0983

Basic information

TDR Targets ID: 6762
Mycobacterium tuberculosis, Probable serine protease PepD (serine proteinase) (MTB32B)

Source Database / ID:  Tuberculist 

pI: 6.2706 | Length (AA): 464 | MW (Da): 46453 | Paralog Number: 1

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 1

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

PF13180   PDZ domain
PF13365   Trypsin-like peptidase domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  
GO:0004252   serine-type endopeptidase activity  
GO:0003824   catalytic activity  
GO:0006508   proteolysis  

Metabolic Pathways

Structural information

Modbase 3D models:

There are 2 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
154 462 1y8t (A) 6 314 99.99 0 1 1.75485 -0.86
406 464 4jj0 (A) 131 186 18.00 0.18 0.61 0.404255 -0.98

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:

  • 1Y8T:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 2Z9I:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 5XDY:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 5ZVJ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 6IEO:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase, Dormant phase. hasan murphy
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_126815)

Species Accession Gene Product
Arabidopsis thaliana AT5G27660   Trypsin family protein with PDZ domain
Arabidopsis thaliana AT3G27925   DegP protease 1
Arabidopsis thaliana AT5G39830   protease DEG 8
Chlamydia trachomatis CT_823   DO serine protease
Drosophila melanogaster Dmel_CG8464   CG8464 gene product from transcript CG8464-RB
Escherichia coli b3234   serine endoprotease, periplasmic
Escherichia coli b0161   serine endoprotease (protease Do), membrane-associated
Homo sapiens ENSG00000166033   HtrA serine peptidase 1
Homo sapiens ENSG00000115317   HtrA serine peptidase 2
Homo sapiens ENSG00000169495   HtrA serine peptidase 4
Homo sapiens ENSG00000170801   HtrA serine peptidase 3
Mycobacterium leprae ML1078   PROBABLE SERINE PROTEASE HTRA (DEGP PROTEIN)
Mycobacterium leprae ML0176   Probable serine protease (serine proteinase)
Mus musculus ENSMUSG00000006205   HtrA serine peptidase 1
Mus musculus 330723   HtrA serine peptidase 4
Mus musculus ENSMUSG00000068329   HtrA serine peptidase 2
Mus musculus ENSMUSG00000029096   HtrA serine peptidase 3
Mycobacterium tuberculosis Rv0983   Probable serine protease PepD (serine proteinase) (MTB32B)
Mycobacterium tuberculosis Rv1223   Probable serine protease HtrA (DEGP protein)
Mycobacterium ulcerans MUL_0668   serine protease
Mycobacterium ulcerans MUL_4517   serine protease HtrA (DegP protein)
Mycobacterium ulcerans MUL_4699   serine protease PepD
Neospora caninum NCLIV_025000   hypothetical protein
Oryza sativa 4350193   Os11g0246600
Oryza sativa 4339651   Os05g0568900
Oryza sativa 9268615   Os04g0459900
Plasmodium berghei PBANKA_1425300   trypsin-like serine protease, putative
Plasmodium berghei PBANKA_1425350   GTPase, putative
Plasmodium falciparum PF3D7_0812220   GTPase, putative
Plasmodium falciparum PF3D7_0812200   trypsin-like serine protease, putative
Plasmodium knowlesi PKNH_1428400   trypsin-like serine protease, putative
Plasmodium knowlesi PKNH_1428500   GTPase, putative
Plasmodium vivax PVX_123158   trypsin-like serine protease, putative
Plasmodium vivax PVX_123162   GTPase, putative
Plasmodium yoelii PY01797   Serine protease Do
Schmidtea mediterranea mk4.006341.03  
Schmidtea mediterranea mk4.000739.01   Serine protease HTRA2, mitochondrial
Schmidtea mediterranea mk4.011296.00  
Treponema pallidum TP0841   periplasmic serine protease DO (htrA-2)
Treponema pallidum TP0546   periplasmic serine protease
Treponema pallidum TP0773   periplasmic serine protease DO (htrA-1)
Wolbachia endosymbiont of Brugia malayi Wbm0770   serine protease

Essentiality

Rv0983 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b0161 Escherichia coli non-essential goodall
b3234 Escherichia coli non-essential goodall
PBANKA_1425300 Plasmodium berghei Dispensable plasmo
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • 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
  • 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
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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

No enough druggable targets predicted through repurposing network model to make a plot

Putative Drugs List


Compound Raw Global Species
0.001 0.5 0.5

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

96 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 Rv0983 (Mycobacterium tuberculosis), Probable serine protease PepD (serine proteinase) (MTB32B)
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