Detailed view for Rv3001c

Basic information

TDR Targets ID: 6253
Mycobacterium tuberculosis, Probable KETOL-acid reductoisomerase IlvC (acetohydroxy-acid isomeroreductase) (alpha-keto-beta-hydroxylacil reductoisomerase)
Source Database / ID:  Tuberculist 

pI: 4.8014 | Length (AA): 333 | MW (Da): 36090 | 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

PF01450   Acetohydroxy acid isomeroreductase, catalytic domain
PF07991   Acetohydroxy acid isomeroreductase, NADPH-binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0050661   NADP binding  
GO:0016491   oxidoreductase activity  
GO:0005488   binding  
GO:0004455   ketol-acid reductoisomerase activity  
GO:0003824   catalytic activity  
GO:0055114   oxidation reduction  
GO:0009082   branched chain family amino acid biosynthetic process  
GO:0008652   amino acid biosynthetic process  
GO:0008152   metabolic process  

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
1 325 4ypo (A) 1 325 99.99 0 1 2.16098 -0.93
16 98 3qha (A) 13 94 28.00 0 0.99 0.733149 -1.51

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
  • 4YPO:
  • 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 20-40% 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_129100)

Species Accession Gene Product
Arabidopsis thaliana AT3G58610   ketol-acid reductoisomerase
Candida albicans CaO19.7733   similar to S. cerevisiae ILV5 (YLR355C) mitochondrial ketol-acid reductoisomerase involved in branched chain aa biosynthesis
Candida albicans CaO19.88   similar to S. cerevisiae ILV5 (YLR355C) mitochondrial ketol-acid reductoisomerase involved in branched chain aa biosynthesis
Escherichia coli b3774   ketol-acid reductoisomerase, NAD(P)-binding
Mycobacterium leprae ML1694c   PROBABLE KETOL-ACID REDUCTOISOMERASE ILVC (Acetohydroxy-acid isomeroreductase) (Alpha-keto-beta-hydroxylacil reductoisomerase)
Mycobacterium tuberculosis Rv3001c   Probable KETOL-acid reductoisomerase IlvC (acetohydroxy-acid isomeroreductase) (alpha-keto-beta-hydroxylacil reductoisomerase)
Mycobacterium ulcerans MUL_1949   ketol-acid reductoisomerase
Oryza sativa 4325375   Os01g0652600
Oryza sativa 9268230   Os10g0446800
Oryza sativa 4339677   Os05g0573700
Saccharomyces cerevisiae YLR355C   ketol-acid reductoisomerase

Essentiality

Rv3001c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3052 this record Mycobacterium tuberculosis essential nmpdr
b3774 Escherichia coli non-essential goodall
YLR355C Saccharomyces cerevisiae inviable yeastgenome
Show/Hide essentiality data references
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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

No reagent availability information for this target.

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

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Gene identifier Rv3001c (Mycobacterium tuberculosis), Probable KETOL-acid reductoisomerase IlvC (acetohydroxy-acid isomeroreductase) (alpha-keto-beta-hydroxylacil reductoisomerase)
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