Detailed view for Rv0189c

Basic information

TDR Targets ID: 6254
Mycobacterium tuberculosis, Probable dihydroxy-acid dehydratase IlvD (dad)

Source Database / ID: Tuberculist / Rv0189c 

pI: 4.8699 | Length (AA): 575 | MW (Da): 59352 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Pfam domains

PF00920   Dehydratase family

Gene Ontology

Mouse over links to read term descriptions.
GO:0004160   dihydroxy-acid dehydratase activity  
GO:0003824   catalytic activity  
GO:0009082   branched chain family amino acid biosynthetic process  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
4 574 5ze4 (A) 6 572 47.00 0 1 1.62494 -0.79

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:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Shows this level of upregulation in
This gene ranks in the upper 60-80% group of genes. Dormant phase.
Upregulation Percent Ranking Shows this level of upregulation in
This gene ranks in the mid 40-60% group of genes. Dormant phase.
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_128618)

Species Accession Gene Product
Arabidopsis thaliana AT3G23940   dehydratase family protein
Candida albicans CaO19.4040   Dihydroxyacid dehydratase
Candida albicans CaO19.11523   Dihydroxyacid dehydratase
Escherichia coli b3771   dihydroxyacid dehydratase
Mycobacterium leprae ML2608c   PROBABLE DIHYDROXY-ACID DEHYDRATASE ILVD (DAD)
Mycobacterium tuberculosis Rv0189c this record   Probable dihydroxy-acid dehydratase IlvD (dad)
Mycobacterium ulcerans MUL_1082   dihydroxy-acid dehydratase
Oryza sativa 4346318   Os08g0559600
Saccharomyces cerevisiae YJR016C   dihydroxy-acid dehydratase ILV3
Schmidtea mediterranea mk4.052640.00  

Essentiality

Rv0189c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu190 this record Mycobacterium tuberculosis essential nmpdr
b3771 Escherichia coli non-essential goodall
YJR016C Saccharomyces cerevisiae inviable yeastgenome
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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 log in using your TDR Targets username and password and send them to us using the corresponding form in this page (only visible to registered users) or 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
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 Rv0189c (Mycobacterium tuberculosis), Probable dihydroxy-acid dehydratase IlvD (dad)
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