Detailed view for Rv2448c

Basic information

TDR Targets ID: 10029
Mycobacterium tuberculosis, Probable valyl-tRNA synthase protein ValS (valyl-tRNA synthetase) (valine--tRNA ligase) (valine translase)
Source Database / ID:  Tuberculist 

pI: 4.9293 | Length (AA): 876 | MW (Da): 97821 | 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

PF00133   tRNA synthetases class I (I, L, M and V)
PF08264   Anticodon-binding domain of tRNA
PF10458   Valyl tRNA synthetase tRNA binding arm

Gene Ontology

Mouse over links to read term descriptions.
GO:0002161   GO:aminoacyl-tRNA editing activity  

GO:0005737   cytoplasm  
GO:0005524   ATP binding  
GO:0004832   valine-tRNA ligase activity  
GO:0004812   aminoacyl-tRNA ligase activity  
GO:0000166   nucleotide binding  
GO:0006438   valyl-tRNA aminoacylation  
GO:0006418   tRNA aminoacylation for protein translation  
GO:0006412   translation  

Structural information

Modbase 3D models:

There are 3 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
2 875 1gax (A) 3 861 46.00 0 1 1.50552 -0.29
195 330 5agr (A) 313 508 26.00 0 1 0.0696511 -0.76
574 809 4xkz (A) 632 881 27.00 0 1 0.649906 -0.96

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 20-40% 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_126723)

Species Accession Gene Product
Arabidopsis thaliana AT1G14610   Valyl-tRNA synthetase
Arabidopsis thaliana AT5G16715   protein EMBRYO DEFECTIVE 2247
Babesia bovis BBOV_III008390   valyl-tRNA synthetase, putative
Brugia malayi Bm1_32860   Valyl-tRNA synthetase
Candida albicans CaO19.1295   probable tRNA synthetase similar to S. cerevisiae VAS1 (YGR094W) valyl-tRNA synthetase
Candida albicans CaO19.8875   probable tRNA synthetase similar to S. cerevisiae VAS1 (YGR094W) valyl-tRNA synthetase
Caenorhabditis elegans CELE_Y87G2A.5   Protein VARS-2
Cryptosporidium hominis Chro.80361   valyl tRNA synthetase
Cryptosporidium parvum cgd8_3100   valyl-tRNA synthetase
Chlamydia trachomatis CT_302   valine--tRNA ligase
Dictyostelium discoideum DDB_G0277733   valine-tRNA ligase
Dictyostelium discoideum DDB_G0288939   valine-tRNA ligase
Drosophila melanogaster Dmel_CG4062   Valyl-tRNA synthetase
Drosophila melanogaster Dmel_CG5660   CG5660 gene product from transcript CG5660-RB
Escherichia coli b4258   valyl-tRNA synthetase
Echinococcus granulosus EgrG_000435000   valyl tRNA synthetase
Echinococcus granulosus EgrG_000527000   valyl tRNA synthetase
Entamoeba histolytica EHI_033680   valyl-tRNA synthetase, putative
Entamoeba histolytica EHI_071580   valyl tRNA synthetase, putative
Echinococcus multilocularis EmuJ_000435000   valyl tRNA synthetase
Echinococcus multilocularis EmuJ_000527000   valyl tRNA synthetase
Giardia lamblia GL50803_35428   Valine-tRNA ligase
Homo sapiens ENSG00000204394   valyl-tRNA synthetase
Homo sapiens ENSG00000137411   valyl-tRNA synthetase 2, mitochondrial
Leishmania braziliensis LbrM.30.3120   valyl-tRNA synthetase, putative
Leishmania donovani LdBPK_303170.1   valyl-tRNA synthetase, putative
Leishmania infantum LinJ.30.3170   valyl-tRNA synthetase, putative
Leishmania major LmjF.30.3130   valyl-tRNA synthetase, putative
Leishmania mexicana LmxM.29.3130   valyl-tRNA synthetase, putative
Loa Loa (eye worm) LOAG_09899   hypothetical protein
Loa Loa (eye worm) LOAG_13027   VRS-2 protein
Loa Loa (eye worm) LOAG_10315   hypothetical protein
Loa Loa (eye worm) LOAG_10316   hypothetical protein
Mycobacterium leprae ML1472c   PROBABLE VALYL-tRNA SYNTHASE PROTEIN VALS (VALYL-tRNA SYNTHETASE) (VALINE--tRNA LIGASE) (VALINE TRANSLASE) ELONGS TO CLASS-I AMI
Mus musculus ENSMUSG00000038838   valyl-tRNA synthetase 2, mitochondrial (putative)
Mus musculus ENSMUSG00000007029   valyl-tRNA synthetase
Mycobacterium tuberculosis Rv2448c   Probable valyl-tRNA synthase protein ValS (valyl-tRNA synthetase) (valine--tRNA ligase) (valine translase)
Mycobacterium ulcerans MUL_3719   valyl-tRNA synthetase
Neospora caninum NCLIV_007730   Valyl-tRNA synthetase, mitochondrial, related
Oryza sativa 4332758   Os03g0335600
Oryza sativa 9271386   Os03g0111700
Oryza sativa 9267455   Os10g0506200
Oryza sativa 4333799   Os03g0694900
Onchocerca volvulus OVOC13489  
Plasmodium berghei PBANKA_1325600   valine--tRNA ligase, putative
Plasmodium falciparum PF3D7_1461900   valine--tRNA ligase, putative
Plasmodium knowlesi PKNH_1219800   valine--tRNA ligase, putative
Plasmodium vivax PVX_117360   valine--tRNA ligase, putative
Plasmodium yoelii PY00514   valyl-tRNA synthetase
Saccharomyces cerevisiae YGR094W   valine--tRNA ligase
Schistosoma japonicum Sjp_0068870   Valyl-tRNA synthetase, putative
Schistosoma japonicum Sjp_0002700   ko:K01873 valyl-tRNA synthetase [EC6.1.1.9], putative
Schistosoma mansoni Smp_097590   valine-tRNA ligase
Schistosoma mansoni Smp_096270   valine-tRNA ligase
Schmidtea mediterranea mk4.002285.04   ValineALQ-tRNA ligase
Schmidtea mediterranea mk4.053068.00  
Schmidtea mediterranea mk4.002725.03   ValineALQ-tRNA ligase, mitochondrial
Trypanosoma brucei gambiense Tbg972.6.4260   valyl-tRNA synthetase, putative
Trypanosoma brucei Tb927.6.4480   valyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.509167.100   valyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.510443.9   valyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.504257.70   valyl-tRNA synthetase, putative
Toxoplasma gondii TGME49_253290   valyl-tRNA synthetase
Treponema pallidum TP1035   valyl-tRNA synthetase
Theileria parva TP04_0740   valyl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_606020   isoleucyl, leucyl, tyrosyl, valyl and methionyl-tRNA synthetases, putative
Trichomonas vaginalis TVAG_102550   valyl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_271200   leucyl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_271210   valyl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_043910   valyl-tRNA synthetase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0786   valyl-tRNA synthetase

Essentiality

Rv2448c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2491 this record Mycobacterium tuberculosis essential nmpdr
Tb927.6.4480 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.6.4480 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.6.4480 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.6.4480 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b4258 Escherichia coli essential goodall
CELE_Y87G2A.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y87G2A.5 Caenorhabditis elegans larval arrest wormbase
CELE_Y87G2A.5 Caenorhabditis elegans slow growth wormbase
CELE_Y87G2A.5 Caenorhabditis elegans sterile wormbase
YGR094W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1325600 Plasmodium berghei Essential plasmo
TGME49_253290 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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): 0.7

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
Homo sapiens valyl-tRNA synthetase Compounds References
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

3 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier Rv2448c (Mycobacterium tuberculosis), Probable valyl-tRNA synthase protein ValS (valyl-tRNA synthetase) (valine--tRNA ligase) (valine translase)
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