Detailed view for Rv3838c

Basic information

TDR Targets ID: 981823
Mycobacterium tuberculosis, Prephenate dehydratase PheA
Source Database / ID:  Tuberculist 

pI: 5.0288 | Length (AA): 321 | MW (Da): 33601 | Paralog Number: 0

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

PF00800  
PF01842  

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0016597   amino acid binding  
GO:0004664   prephenate dehydratase activity  
GO:0004106   chorismate mutase activity  
GO:0009094   L-phenylalanine biosynthetic process  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There are 2 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
2 305 3mwb (A) 4 309 41.00 0 1 1.36824 -0.17
203 276 5fii (A) 36 109 30.00 0 0.61 0.57773 -0.58

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_128434)

Species Accession Gene Product
Arabidopsis thaliana AT1G11790   arogenate dehydratase 1
Arabidopsis thaliana AT2G27820   arogenate dehydratase 3
Arabidopsis thaliana AT1G08250   arogenate dehydratase 6
Arabidopsis thaliana AT3G07630   arogenate dehydratase 2
Candida albicans CaO19.7864   likely prephenate dehydratase similar to S. cerevisiae PHA2 (YNL316C) involved in phenylalanine biosynthesis
Candida albicans CaO19.234   likely prephenate dehydratase similar to S. cerevisiae PHA2 (YNL316C) involved in phenylalanine biosynthesis
Escherichia coli b2599   chorismate mutase and prephenate dehydratase, P-protein
Mycobacterium leprae ML0078   Possible prephenate dehydratase PheA
Mycobacterium tuberculosis Rv3838c   Prephenate dehydratase PheA
Mycobacterium ulcerans MUL_5011   prephenate dehydratase
Oryza sativa 4347877   Os09g0566000
Oryza sativa 4347875   Os09g0565700
Oryza sativa 4332477   Os03g0286200
Oryza sativa 4335756   Os04g0406600
Oryza sativa 9270024   Os02g0478525
Oryza sativa 4349157   Os10g0523700
Oryza sativa 4344396   Os07g0694600
Saccharomyces cerevisiae YNL316C   prephenate dehydratase PHA2
Schmidtea mediterranea mk4.005675.00  
Schmidtea mediterranea mk4.054491.01  

Essentiality

Rv3838c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b2599 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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

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.

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 Rv3838c (Mycobacterium tuberculosis), Prephenate dehydratase PheA
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