Detailed view for Rv3336c

Basic information

TDR Targets ID: 9992
Mycobacterium tuberculosis, Probable tryptophanyl-tRNA synthetase TrpS (tryptophan--tRNA ligase) (TRPRS) (tryptophan translase)
Source Database / ID:  Tuberculist 

pI: 4.9213 | Length (AA): 336 | MW (Da): 36272 | 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

PF00579   tRNA synthetases class I (W and Y)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0005524   ATP binding  
GO:0004830   tryptophan-tRNA ligase activity  
GO:0004812   aminoacyl-tRNA ligase activity  
GO:0000166   nucleotide binding  
GO:0006436   tryptophanyl-tRNA aminoacylation  
GO:0006418   tRNA aminoacylation for protein translation  
GO:0006412   translation  

Metabolic Pathways

Tryptophan metabolism (KEGG)
Aminoacyl-tRNA biosynthesis (KEGG)

Structural information

Modbase 3D models:

There are 4 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
2 335 3sz3 (A) 0 335 48.00 0 1 1.64085 -1.15
7 335 3n9i (A) 15 343 52.00 0 1 1.65937 -1.17
7 335 5ekd (A) 34 360 43.00 0 1 1.56637 -1.14
8 335 1i6k (A) 2 325 51.00 0 1 1.68099 -1.31

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

Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase, Dormant phase. hasan murphy
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_127531)

Species Accession Gene Product
Arabidopsis thaliana AT2G25840   protein ovule abortion 4
Babesia bovis BBOV_III008750   tRNA synthetases class I (W and Y) family protein
Brugia malayi Bm1_45970   tryptophanyl-tRNA synthetase family protein
Candida albicans CaO19.11775   Tryptophanyl-tRNA synthetase, mitochondrial
Candida albicans CaO19.4299   Tryptophanyl-tRNA synthetase, mitochondrial
Caenorhabditis elegans CELE_C34E10.4   Protein PRX-10, isoform A
Chlamydia trachomatis CT_585   tryptophan--tRNA ligase
Dictyostelium discoideum DDB_G0274567   tryptophan-tRNA ligase
Drosophila melanogaster Dmel_CG7441   CG7441 gene product from transcript CG7441-RA
Escherichia coli b3384   tryptophanyl-tRNA synthetase
Echinococcus granulosus EgrG_000759100   tryptophanyl tRNA synthetase
Echinococcus multilocularis EmuJ_000759100   tryptophanyl tRNA synthetase
Homo sapiens ENSG00000116874   tryptophanyl tRNA synthetase 2, mitochondrial
Loa Loa (eye worm) LOAG_08050   hypothetical protein
Mycobacterium leprae ML0686   Probable tryptophanyl-tRNA synthetase TrpS (TRYPTOPHAN--TRNA LIGASE) (TRPRS) (TRYPTOPHAN TRANSLASE)
Mus musculus ENSMUSG00000004233   tryptophanyl tRNA synthetase 2 (mitochondrial)
Mycobacterium tuberculosis Rv3336c   Probable tryptophanyl-tRNA synthetase TrpS (tryptophan--tRNA ligase) (TRPRS) (tryptophan translase)
Mycobacterium ulcerans MUL_1441   tryptophanyl-tRNA synthetase
Neospora caninum NCLIV_008400   Tryptophanyl-tRNA synthetase (EC 6.1.1.2), related
Oryza sativa 4326551   Os01g0743400
Plasmodium berghei PBANKA_1464700   tryptophan--tRNA ligase, putative
Plasmodium falciparum PF3D7_1251700   tryptophan--tRNA ligase
Plasmodium knowlesi PKNH_1471700   tryptophan--tRNA ligase, putative
Plasmodium vivax PVX_101475   tryptophan--tRNA ligase, putative
Saccharomyces cerevisiae YDR268W   tryptophan--tRNA ligase MSW1
Schistosoma japonicum Sjp_0092060   ko:K01867 tryptophanyl-tRNA synthetase [EC6.1.1.2], putative
Schistosoma mansoni Smp_150680   tryptophanyl-tRNA synthetase
Schmidtea mediterranea mk4.047565.00  
Schmidtea mediterranea mk4.003780.00   TryptophanALQ-tRNA ligase, mitochondrial
Schmidtea mediterranea mk4.005577.02   TryptophanALQ-tRNA ligase, mitochondrial
Toxoplasma gondii TGME49_254110   tryptophanyl-tRNA synthetase (TrpRS1)
Treponema pallidum TP0632   tryptophanyl-tRNA synthetase
Theileria parva TP04_0776   Tryptophanyl-tRNA synthetase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0534   tryptophanyl-tRNA synthetase

Essentiality

Rv3336c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3396 this record Mycobacterium tuberculosis essential nmpdr
b3384 Escherichia coli essential goodall
CELE_C34E10.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_C34E10.4 Caenorhabditis elegans slow growth wormbase
TGME49_254110 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • 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.
  • 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
  • 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
  • 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): 0.2

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 Rv3336c (Mycobacterium tuberculosis), Probable tryptophanyl-tRNA synthetase TrpS (tryptophan--tRNA ligase) (TRPRS) (tryptophan translase)
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