Detailed view for Rv1745c

Basic information

TDR Targets ID: 6245
Mycobacterium tuberculosis, Probable isopentenyl-diphosphate delta-isomerase Idi (IPP isomerase) (isopentenyl pyrophosphate isomerase)
Source Database / ID:  Tuberculist 

pI: 7.6451 | Length (AA): 203 | MW (Da): 22490 | 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

PF00293   NUDIX domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016787   hydrolase activity  
GO:0004452   isopentenyl-diphosphate delta-isomerase activity  
GO:0008299   isoprenoid 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
12 175 1ppv (A) 4 166 46.00 0 1 1.46228 -1.16

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 Stage Dataset
Mid 40-60% 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_128735)

Species Accession Gene Product
Arabidopsis thaliana AT3G02780   Isopentenyl-diphosphate Delta-isomerase II
Arabidopsis thaliana AT5G16440   Isopentenyl-diphosphate Delta-isomerase I
Brugia malayi Bm1_16940   isopentenyl-diphosphate delta-isomerase, type 1 family protein
Candida albicans CaO19.4558   similar to N terminus of isopentenyl diphosphate isomerase of isoprenoid biosynthetic pathway
Candida albicans CaO19.12027   similar to N terminus of isopentenyl diphosphate isomerase of isoprenoid biosynthetic pathway
Candida albicans CaO19.10291   similar to isopentenyl diphosphate isomerase of isoprenoid biosynthetic pathway (MutT/NUDIX domain)
Candida albicans CaO19.2775   similar to isopentenyl diphosphate isomerase of isoprenoid biosynthetic pathway (MutT/NUDIX domain)
Caenorhabditis elegans CELE_K06H7.9   Protein IDI-1
Dictyostelium discoideum DDB_G0290011   IDP isomerase
Drosophila melanogaster Dmel_CG5919   CG5919 gene product from transcript CG5919-RA
Escherichia coli b2889   isopentenyl diphosphate isomerase
Echinococcus granulosus EgrG_000463100   isopentenyl diphosphate delta isomerase
Echinococcus multilocularis EmuJ_000463100   isopentenyl diphosphate delta isomerase
Giardia lamblia GL50803_6335   Isopentenyl-diphosphate delta-isomerase 1
Homo sapiens ENSG00000067064   isopentenyl-diphosphate delta isomerase 1
Loa Loa (eye worm) LOAG_03393   isopentenyl-diphosphate delta-isomerase
Mus musculus ENSMUSG00000058258   isopentenyl-diphosphate delta isomerase
Mus musculus 102635781   isopentenyl-diphosphate Delta-isomerase 1-like
Mycobacterium tuberculosis Rv1745c   Probable isopentenyl-diphosphate delta-isomerase Idi (IPP isomerase) (isopentenyl pyrophosphate isomerase)
Oryza sativa 4343523   Os07g0546000
Oryza sativa 4338791   Os05g0413400
Saccharomyces cerevisiae YPL117C   isopentenyl-diphosphate delta-isomerase IDI1
Schistosoma japonicum Sjp_0304050   ko:K01823 isopentenyl-diphosphate delta-isomerase [EC5.3.3.2], putative
Schistosoma japonicum Sjp_0086190   ko:K03134 transcription initiation factor TFIID subunit D8, putative
Schistosoma mansoni Smp_130430   isopentenyl-diphosphate delta-isomerase
Schmidtea mediterranea mk4.001073.07   Isopentenyl-diphosphate isomerase
Trichomonas vaginalis TVAG_116230   isopentenyl-diphosphate delta isomerase, putative
Trichomonas vaginalis TVAG_495540   isopentenyl-diphosphate delta isomerase, putative

Essentiality

Rv1745c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1775 this record Mycobacterium tuberculosis non-essential nmpdr
b2889 Escherichia coli non-essential goodall
YPL117C Saccharomyces cerevisiae inviable yeastgenome
Show/Hide essentiality data references
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.

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
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 Rv1745c (Mycobacterium tuberculosis), Probable isopentenyl-diphosphate delta-isomerase Idi (IPP isomerase) (isopentenyl pyrophosphate isomerase)
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