Detailed view for Rv2178c

Basic information

TDR Targets ID: 5684
Mycobacterium tuberculosis, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG (DAHP synthetase, phenylalanine-repressible)
Source Database / ID:  Tuberculist 

pI: 5.5542 | Length (AA): 462 | MW (Da): 50641 | 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

PF01474   Class-II DAHP synthetase family

Gene Ontology

Mouse over links to read term descriptions.
GO:0003849   3-deoxy-7-phosphoheptulonate synthase activity  
GO:0003824   catalytic activity  
GO:0009073   aromatic amino acid family 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
1 462 5e5g (A) 1 462 99.99 0 1 2.2392 -1.49

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
  • 2B7O:
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  • 2W19:
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  • 2W1A:
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  • 2YPO:
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  • 2YPP:
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  • 2YPQ:
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  • 3KGF:
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  • 3NUD:
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  • 3NUE:
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  • 3NV8:
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  • 3PFP:
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  • 3RZI:
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  • 5CKV:
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  • 5CKX:
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  • 5E2L:
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  • 5E40:
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PDB tag
  • 5E4N:
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PDB tag
  • 5E5G:
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PDB tag
  • 5E7Z:
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PDB tag
  • 5EX4:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Lower 0-20% 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_130802)

Species Accession Gene Product
Arabidopsis thaliana AT1G22410   Class-II DAHP synthetase family protein
Arabidopsis thaliana AT4G33510   3-deoxy-d-arabino-heptulosonate 7-phosphate synthase
Arabidopsis thaliana AT4G39980   3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 1
Mycobacterium leprae ML0896   Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG (DAHP synthetase, phenylalanine-repressible)
Mycobacterium tuberculosis Rv2178c   3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG (DAHP synthetase, phenylalanine-repressible)
Mycobacterium ulcerans MUL_3533   3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
Neospora caninum NCLIV_004821   Phospho-2-dehydro-3-deoxyheptonate aldolase, related
Oryza sativa 4345872   Os08g0484500
Oryza sativa 4333014   Os03g0389700
Oryza sativa 4343946   Os07g0622200
Oryza sativa 4349410   Os10g0564400
Toxoplasma gondii TGME49_221260   Class-II DAHP synthetase family protein

Essentiality

Rv2178c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2212 this record Mycobacterium tuberculosis essential nmpdr
TGME49_221260 Toxoplasma gondii Probably essential sidik
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
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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

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 Rv2178c (Mycobacterium tuberculosis), 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG (DAHP synthetase, phenylalanine-repressible)
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