Detailed view for Rv2987c

Basic information

TDR Targets ID: 6291
Mycobacterium tuberculosis, Probable 3-isopropylmalate dehydratase (small subunit) LeuD (isopropylmalate isomerase) (alpha-IPM isomerase) (IPMI)
Source Database / ID:  Tuberculist 

pI: 4.8855 | Length (AA): 198 | MW (Da): 21780 | 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

PF00694   Aconitase C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0009316   3-isopropylmalate dehydratase complex  
GO:0003861   3-isopropylmalate dehydratase activity  
GO:0008152   metabolic process  
GO:0009098   leucine biosynthetic 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
2 168 3h5j (A) 2 168 99.99 0 1 2.14793 -2.13

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
  • 3H5E:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3H5H:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3H5J:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Dormant phase, Dormant phase. hasan 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_130205)

Species Accession Gene Product
Arabidopsis thaliana AT2G43100   isopropylmalate isomerase 2
Arabidopsis thaliana AT3G58990   isopropylmalate isomerase 1
Arabidopsis thaliana AT2G43090   Aconitase/3-isopropylmalate dehydratase protein
Escherichia coli b0071   3-isopropylmalate dehydratase small subunit
Mycobacterium leprae ML1684c   PROBABLE 3-ISOPROPYLMALATE DEHYDRATASE (SMALL SUBUNIT) LEUD (ISOPROPYLMALATE ISOMERASE) (ALPHA-IPM ISOMERASE) (IPMI)
Mycobacterium tuberculosis Rv2987c   Probable 3-isopropylmalate dehydratase (small subunit) LeuD (isopropylmalate isomerase) (alpha-IPM isomerase) (IPMI)
Mycobacterium ulcerans MUL_1969   isopropylmalate isomerase small subunit
Oryza sativa 4330192   Os02g0655300

Essentiality

Rv2987c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3037 this record Mycobacterium tuberculosis essential nmpdr
b0071 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
growth (GO:0040007) decreased (PATO:0000468) inferred from animal model system (ECO:0000179) Mycobacterium bovis No drug identifiers listed for this gene.
Annotator: crowther@u.washington.edu. Comment: 2008-01-02. References: 7868221
growth (GO:0040007) auxotroph (PATO:0000422) inferred from in vitro culture assay (ECO:0000182) Mycobacterium bovis No drug identifiers listed for this gene.
Annotator: crowther@u.washington.edu. Comment: 2008-01-02. References: 7868221
growth (GO:0040007) decreased (PATO:0000468) inferred from in vitro culture assay (ECO:0000182) Mycobacterium bovis No drug identifiers listed for this gene.
Annotator: crowther@u.washington.edu. Comment: 2008-01-02. References: 10768986 8613393
growth (GO:0040007) decreased (PATO:0000468) inferred from animal model system (ECO:0000179) Mycobacterium tuberculosis No drug identifiers listed for this gene.
Annotator: crowther@u.washington.edu. Comment: 2008-01-02. References: 10768986

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
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

5 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 Rv2987c (Mycobacterium tuberculosis), Probable 3-isopropylmalate dehydratase (small subunit) LeuD (isopropylmalate isomerase) (alpha-IPM isomerase) (IPMI)
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