Detailed view for Rv2538c

Basic information

TDR Targets ID: 5680
Mycobacterium tuberculosis, 3-dehydroquinate synthase AroB
Source Database / ID:  Tuberculist 

pI: 5.1236 | Length (AA): 362 | MW (Da): 38119 | Paralog Number: 1

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG2

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

PF01761   3-dehydroquinate synthase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016838   carbon-oxygen lyase activity, acting on phosphates  
GO:0005737   cytoplasm  
GO:0003856   3-dehydroquinate synthase activity  
GO:0009073   aromatic amino acid family biosynthetic process  
GO:0009058   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
6 361 3qbe (A) 6 361 99.99 0 1 2.22213 -1.62

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
  • 3QBD:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3QBE:
  • 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
  • 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_127183)

Species Accession Gene Product
Arabidopsis thaliana AT2G45300   3-phosphoshikimate 1-carboxyvinyltransferase / 5-enolpyruvylshikimate-3-phosphate / EPSP synthase
Arabidopsis thaliana AT1G48860   putative 5-enolpyruvylshikimate-3-phosphate synthase
Arabidopsis thaliana AT5G66120   putative 3-dehydroquinate synthase
Candida albicans CaO19.12175   similar to S. cerevisiae ARO1 pentafunctional aromatic amino acid family biosynthesis protein
Candida albicans CaO19.4704   similar to S. cerevisiae ARO1 pentafunctional aromatic amino acid family biosynthesis protein
Chlamydia trachomatis CT_366   phosphoshikimate 1-carboxyl vinyltransferase
Chlamydia trachomatis CT_369   dehyroquinate synthase
Escherichia coli b3389   3-dehydroquinate synthase
Escherichia coli b0908   5-enolpyruvylshikimate-3-phosphate synthetase
Mycobacterium leprae ML0792c   probable 3-phosphoshikimate 1-carboxyvinyl transferase AroA (5-ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE) (EPSP SYNTHASE) (EPSPS
Mycobacterium leprae ML0518   3-dehydroquinate synthase AroB
Mycobacterium tuberculosis Rv3227   3-phosphoshikimate 1-carboxyvinyltransferase AroA (5-enolpyruvylshikimate-3-phosphate synthase) (EPSP synthase) (EPSPS)
Mycobacterium tuberculosis Rv2538c   3-dehydroquinate synthase AroB
Mycobacterium ulcerans MUL_2560   3-phosphoshikimate 1-carboxyvinyltransferase
Mycobacterium ulcerans MUL_1761   3-dehydroquinate synthase
Neospora caninum NCLIV_053120   3-dehydroquinate synthase (EC 4.2.3.4), related
Oryza sativa 4347717   Os09g0539100
Oryza sativa 4340026   Os06g0133900
Saccharomyces cerevisiae YDR127W   pentafunctional protein ARO1p
Schistosoma mansoni Smp_109520   3-dehydroquinate synthase
Schmidtea mediterranea mk4.065648.00  
Toxoplasma gondii TGME49_307040   shikimate dehydrogenase substrate binding domain-containing protein

Essentiality

Rv2538c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2582 this record Mycobacterium tuberculosis essential nmpdr
b0908 Escherichia coli non-essential goodall
b3389 Escherichia coli non-essential goodall
TGME49_307040 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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): 0.3

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
Escherichia coli 5-enolpyruvylshikimate-3-phosphate synthetase Compounds References
Escherichia coli 3-dehydroquinate synthase Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0198 0.3863 1
0.0069 0.2848 1
0.0291 0.2808 1
0.0777 0.2711 1
0.0633 0.388 0.4508
0.0668 1 1
0.0199 0.2569 1
0.0114 0.3387 0.5
0.1208 0.3798 1
0.0258 1 1
0.0179 0.3798 1
0.0112 0.3387 0.5
0.0476 0.3757 0.5
0.0777 0.2711 1
0.0706 0.3519 1
0.0258 0.2871 1
0.0363 0.3857 0.5
0.0113 0.2815 0.2962
0.024 0.3632 0.5
0.0206 0.3798 1
0.0211 0.3624 1
0.012 0.3387 0.5
0.0213 0.379 1
0.1208 0.3798 1
0.0258 1 1
0.0159 0.3808 1
0.0139 0.337 1
0.024 0.3833 1
0.0729 0.3729 0.5
0.012 0.3387 0.5
0.0139 0.3342 0.3333
0.0207 0.2636 0.7849
0.0291 0.2808 1
0.0139 0.337 1
0.012 0.3387 0.5
0.0728 0.3755 0.5
0.0633 0.388 0.4508
0.056 0.36 0.36
0.0728 0.3755 0.5
0.0108 0.3841 1
0.0117 0.3311 0.5
0.0152 0.3772 1
0.0258 1 1
0.0695 0.2983 0.3785
0.0207 0.2636 0.7849
0.0258 0.2871 1
0.0849 0.2766 0.5
0.024 0.3833 1

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

3 literature references were collected for this gene.

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Gene identifier Rv2538c (Mycobacterium tuberculosis), 3-dehydroquinate synthase AroB
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