Detailed view for Rv1612

Basic information

TDR Targets ID: 9987
Mycobacterium tuberculosis, Tryptophan synthase, beta subunit TrpB
Source Database / ID:  Tuberculist 

pI: 5.551 | Length (AA): 410 | MW (Da): 43287 | 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

PF00291   Pyridoxal-phosphate dependent enzyme

Gene Ontology

Mouse over links to read term descriptions.
GO:0030170   pyridoxal phosphate binding  
GO:0004834   tryptophan synthase activity  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  
GO:0006568   tryptophan metabolic process  
GO:0000162   tryptophan 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
5 409 5tch (B) 5 409 99.99 0 1 2.2203 -1.39

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
  • 2O2E:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2O2J:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
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  • 5OCW:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5TCF:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5TCG:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
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  • 5TCH:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5TCI:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5TCJ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 6DU1:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 6DUA:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
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  • 6DWE:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 6E9P:
  • 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_128016)

Species Accession Gene Product
Arabidopsis thaliana AT4G27070   tryptophan synthase beta chain
Arabidopsis thaliana AT5G54810   tryptophan synthase beta chain
Arabidopsis thaliana AT5G38530   tryptophan synthase beta chain
Arabidopsis thaliana AT5G28237   tryptophan synthase beta chain-like protein
Candida albicans CaO19.4718   likely tryptophan synthetase alpha chain similar to S. cerevisiae TRP5 (YGL026C)
Cryptosporidium hominis Chro.50503   tryptophan synthase
Cryptosporidium parvum cgd5_4560   tryptophan synthase trpB of possible bacterial origin
Chlamydia trachomatis CT_170   tryptophan synthase subunit beta
Escherichia coli b1261   tryptophan synthase, beta subunit
Mycobacterium leprae ML1272   Probable tryptophan synthase, beta subunit TrpB
Mycobacterium tuberculosis Rv1612   Tryptophan synthase, beta subunit TrpB
Mycobacterium ulcerans MUL_1592   tryptophan synthase subunit beta
Oryza sativa 4344612   Os08g0135900
Saccharomyces cerevisiae YGL026C   tryptophan synthase TRP5

Essentiality

Rv1612 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1640 this record Mycobacterium tuberculosis essential nmpdr
b1261 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
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

1 literature reference was collected for this gene.

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 Rv1612 (Mycobacterium tuberculosis), Tryptophan synthase, beta subunit TrpB
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