Detailed view for Rv2498c

Basic information

TDR Targets ID: 5750
Mycobacterium tuberculosis, Probable citrate (pro-3S)-lyase (beta subunit) CitE (citrase) (citratase) (citritase) (citridesmolase) (citrase aldolase)
Source Database / ID:  Tuberculist 

pI: 5.0544 | Length (AA): 273 | MW (Da): 28886 | Paralog Number: 1

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

PF03328   HpcH/HpaI aldolase/citrate lyase family

Gene Ontology

Mouse over links to read term descriptions.
GO:0009346   citrate lyase complex  
GO:0016830   carbon-carbon lyase activity  
GO:0003824   catalytic activity  
GO:0006725   aromatic compound metabolic process  

Metabolic Pathways

Citrate cycle (TCA cycle) (KEGG)
Two-component system (KEGG)

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
2 269 6arb (A) 10 277 99.99 0 1 2.17739 -1.01

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
  • 1U5H:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 1U5V:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 1Z6K:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 6AQ4:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 6ARB:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 6AS5:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 6CHU:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 6CJ3:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 6CJ4:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. 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_130136)

Species Accession Gene Product
Caenorhabditis elegans CELE_C01G10.7   Protein C01G10.7
Dictyostelium discoideum DDB_G0284067   citrate lyase subunit beta-like protein
Escherichia coli b0616   citrate lyase, citryl-ACP lyase (beta) subunit
Echinococcus granulosus EgrG_000673750   citrate lyase subunit beta protein
Echinococcus multilocularis EmuJ_000673750   citrate lyase subunit beta protein
Homo sapiens ENSG00000125246   citrate lyase beta like
Mus musculus ENSMUSG00000025545   citrate lyase beta like
Mycobacterium tuberculosis Rv2498c   Probable citrate (pro-3S)-lyase (beta subunit) CitE (citrase) (citratase) (citritase) (citridesmolase) (citrase aldolase)
Mycobacterium tuberculosis Rv3075c   Conserved protein
Mycobacterium ulcerans MUL_4021   citrate (pro-3S)-lyase subunit beta
Mycobacterium ulcerans MUL_3776   citrate (pro-3S)-lyase subunit beta
Mycobacterium ulcerans MUL_3451   citrate lyase beta subunit, CitE_2
Schmidtea mediterranea mk4.003909.00  
Schmidtea mediterranea mk4.010401.01  
Schmidtea mediterranea mk4.003909.01  
Trichomonas vaginalis TVAG_277050   Citrate lyase beta chain, putative

Essentiality

Rv2498c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2541 this record Mycobacterium tuberculosis non-essential nmpdr
Mycobacterium tuberculosis non-essential nmpdr
b0616 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • 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
  • 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
  • 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.

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

  • Assay for Citrate Lyase (4.1.3.6 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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 Rv2498c (Mycobacterium tuberculosis), Probable citrate (pro-3S)-lyase (beta subunit) CitE (citrase) (citratase) (citritase) (citridesmolase) (citrase aldolase)
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