Detailed view for Rv2995c

Basic information

TDR Targets ID: 6289
Mycobacterium tuberculosis, Probable 3-isopropylmalate dehydrogenase LeuB (beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)
Source Database / ID:  Tuberculist 

pI: 5.5387 | Length (AA): 336 | MW (Da): 35306 | 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

PF00180   Isocitrate/isopropylmalate dehydrogenase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016616   oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor  
GO:0003862   3-isopropylmalate dehydrogenase activity  
GO:0051287   NAD binding  
GO:0000287   magnesium ion binding  
GO:0055114   oxidation reduction  
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
2 336 1w0d (A) 2 336 99.99 0 1 2.20462 -1.19

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
  • 1W0D:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2G4O:
  • 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
  • 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_126870)

Species Accession Gene Product
Arabidopsis thaliana AT3G09810   Isocitrate dehydrogenase [NAD] catalytic subunit 6
Arabidopsis thaliana AT5G03290   Isocitrate dehydrogenase [NAD] catalytic subunit 5
Brugia malayi Bm1_13415   isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
Candida albicans CaO19.10060   homoisocitrate dehydrogenase
Candida albicans CaO19.5791   isocitrate dehydrogenase
Candida albicans CaO19.2525   homoisocitrate dehydrogenase
Candida albicans CaO19.13213   isocitrate dehydrogenase
Caenorhabditis elegans CELE_F43G9.1   Protein IDHA-1
Dictyostelium discoideum DDB_G0271344   isocitrate dehydrogenase (NAD+)
Drosophila melanogaster Dmel_CG32026   CG32026 gene product from transcript CG32026-RA
Drosophila melanogaster Dmel_CG12233   lethal (1) G0156
Escherichia coli b1800   D-malate oxidase, NAD-dependent
Escherichia coli b1136   e14 prophage
Entamoeba histolytica EHI_143560   tartrate dehydrogenase, putative
Homo sapiens 3419   isocitrate dehydrogenase 3 (NAD+) alpha
Leishmania braziliensis LbrM.33.2820   isocitrate dehydrogenase, putative
Leishmania donovani LdBPK_332680.1   isocitrate dehydrogenase, putative
Leishmania infantum LinJ.33.2680   isocitrate dehydrogenase, putative
Leishmania major LmjF.33.2550   isocitrate dehydrogenase, putative
Leishmania mexicana LmxM.32.2550   isocitrate dehydrogenase, putative
Loa Loa (eye worm) LOAG_06771   hypothetical protein
Mycobacterium leprae ML1691c   PROBABLE 3-ISOPROPYLMALATE DEHYDROGENASE LEUB (BETA-IPM DEHYDROGENASE) (IMDH) (3-IPM-DH)
Mus musculus ENSMUSG00000032279   isocitrate dehydrogenase 3 (NAD+) alpha
Mycobacterium tuberculosis Rv2995c   Probable 3-isopropylmalate dehydrogenase LeuB (beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)
Mycobacterium ulcerans MUL_1953   3-isopropylmalate dehydrogenase
Oryza sativa 4324442   Os01g0276100
Onchocerca volvulus OVOC6595  
Saccharomyces cerevisiae YOR136W   isocitrate dehydrogenase (NAD(+)) IDH2
Saccharomyces cerevisiae YIL094C   homoisocitrate dehydrogenase
Schmidtea mediterranea mk4.002123.05   Probable isocitrate dehydrogenase
Trichomonas vaginalis TVAG_494040   isocitrate dehydrogenase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0367   isocitrate dehydrogenase

Essentiality

Rv2995c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3045 this record Mycobacterium tuberculosis essential nmpdr
b1136 Escherichia coli essential goodall
b1800 Escherichia coli non-essential goodall
CELE_F43G9.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_F43G9.1 Caenorhabditis elegans slow growth wormbase
CELE_F43G9.1 Caenorhabditis elegans sterile wormbase
CELE_F43G9.1 Caenorhabditis elegans terminal arrest variable wormbase
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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

No assay information for this target.

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Rv2995c cloned gene BRENDA A gene with this EC number or name or sequence has been cloned from Mycobacterium bovis ( 1 )

Bibliographic References

2 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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Rv2995c (Mycobacterium tuberculosis), Probable 3-isopropylmalate dehydrogenase LeuB (beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)
Title for this comment
Comment