Detailed view for Rv1098c

Basic information

TDR Targets ID: 6106
Mycobacterium tuberculosis, Probable fumarase Fum (fumarate hydratase)
Source Database / ID:  Tuberculist 

pI: 5.18 | Length (AA): 474 | MW (Da): 50141 | 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

PF00206   Lyase
PF10415   Fumarase C C-terminus

Gene Ontology

Mouse over links to read term descriptions.
GO:0045239   tricarboxylic acid cycle enzyme complex  
GO:0016829   lyase activity  
GO:0004333   fumarate hydratase activity  
GO:0003824   catalytic activity  
GO:0006106   fumarate metabolic process  
GO:0006099   tricarboxylic acid cycle  

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
6 465 3rrp (A) 3 464 86.00 0 1 2.00776 -0.93

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
  • 3NO9:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4ADL:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4ADM:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4APA:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4APB:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5F91:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5F92:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Mid 40-60% 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_127258)

Species Accession Gene Product
Arabidopsis thaliana AT5G50950   fumarate hydratase 2
Arabidopsis thaliana AT2G47510   fumarate hydratase 1
Brugia malayi Bm1_47480   fumarase
Candida albicans CaO19.14016   fumarate hydratase
Candida albicans CaO19.6724   corresponds to N-terminus of S. cerevisiae FUM1
Candida albicans CaO19.543   fumarate hydratase
Candida albicans CaO19.6725   fumarate hydratase
Candida albicans CaO19.14017   corresponds to N-terminus of S. cerevisiae FUM1
Candida albicans CaO19.8178   fumarate hydratase
Caenorhabditis elegans CELE_H14A12.2   Protein FUM-1, isoform B
Chlamydia trachomatis CT_855   fumarate hydratase
Dictyostelium discoideum DDB_G0280495   fumarate hydratase
Drosophila melanogaster Dmel_CG6140   CG6140 gene product from transcript CG6140-RB
Drosophila melanogaster Dmel_CG4095   CG4095 gene product from transcript CG4095-RA
Drosophila melanogaster Dmel_CG4094   lethal (1) G0255
Escherichia coli b1611   fumarate hydratase (fumarase C),aerobic Class II
Escherichia coli b4139   aspartate ammonia-lyase
Entamoeba histolytica EHI_150390   aspartate ammonia-lyase, putative
Homo sapiens ENSG00000091483   fumarate hydratase
Loa Loa (eye worm) LOAG_03614   fumarase 1
Mycobacterium leprae ML1947   PROBABLE FUMARASE FUM (Fumarate hydratase)
Mus musculus 14194   fumarate hydratase 1
Mycobacterium tuberculosis Rv1098c   Probable fumarase Fum (fumarate hydratase)
Mycobacterium ulcerans MUL_0181   fumarate hydratase
Oryza sativa 4332774   Os03g0337900
Saccharomyces cerevisiae YPL262W   fumarase FUM1
Schistosoma japonicum Sjp_0070590   ko:K01679 fumarate hydratase [EC4.2.1.2B], putative
Schistosoma mansoni Smp_158240   fumarate hydratase
Schmidtea mediterranea mk4.000157.15   AT27305p
Wolbachia endosymbiont of Brugia malayi Wbm0504   fumarate hydratase

Essentiality

Rv1098c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1117 this record Mycobacterium tuberculosis essential nmpdr
b1611 Escherichia coli non-essential goodall
b4139 Escherichia coli non-essential goodall
CELE_H14A12.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_H14A12.2 Caenorhabditis elegans larval arrest wormbase
CELE_H14A12.2 Caenorhabditis elegans slow growth wormbase
Show/Hide essentiality data references
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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
Species Known druggable target Linked compounds Reference
Sus scrofa Fumarate hydratase, mitochondrial Compounds References
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

  • Assay for Fumarase (4.2.1.2 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

4 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.

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Gene identifier Rv1098c (Mycobacterium tuberculosis), Probable fumarase Fum (fumarate hydratase)
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