Detailed view for TGME49_289300

Basic information

TDR Targets ID: 257680
Toxoplasma gondii, methionyl-tRNA synthetase
Source Database / ID:  ToxoDB 

pI: 6.7116 | Length (AA): 976 | MW (Da): 106101 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG5

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

PF01588   Putative tRNA binding domain
PF09334   tRNA synthetases class I (M)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0005524   ATP binding  
GO:0004825   methionine-tRNA ligase activity  
GO:0004812   aminoacyl-tRNA ligase activity  
GO:0000166   nucleotide binding  
GO:0000049   tRNA binding  
GO:0006431   methionyl-tRNA aminoacylation  
GO:0006418   tRNA aminoacylation for protein translation  
GO:0006412   translation  

Structural information

Modbase 3D models:

There are 12 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
118 815 1ffy (A) 171 849 14.00 0 0.95 0.77 0.66
169 728 1iq0 (A) 2 590 11.00 0 0.64 0.33 -0.04
242 956 1gax (A) 3 862 18.00 0 1 0.39 -0.37
272 769 1a8h () 2 499 39.00 0 1 1.14 -1.72
275 736 5k0s (B) 3 471 46.00 0 1 1.07556 -1.1
275 764 4qre (A) 3 512 28.00 0 1 0.856049 -0.3
275 853 1ffy (A) 47 882 21.00 0 1 0.365238 0.23
276 772 2x1l (A) 3 511 44.00 0 1 1.12142 -1.2
784 898 3ers (X) 10 104 33.00 0 1 0.333828 -0.11
784 903 1gd7 (A) 8 108 42.00 0.00022 0.95 0.401151 0.49
785 874 2cwp (A) 14 92 34.00 0.14 0.99 0.414413 -0.21
803 952 1ntg (A) 21 166 19.00 0 0.79 0.275789 0.82

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
Upper 80-100% percentile VEG Tachyzoite. Gregory
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile ME49 Tachyzoite, ME49 merozoite, ME49 Bradyzoite. Gregory Hehl AB Sibley/Greg
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile ME49 Oocyst. Fritz HM
Show/Hide expression data references
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • Gregory ToxoDB
  • Sibley/Greg ToxoDB
  • Hehl AB Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes.

Orthologs

Ortholog group members (OG5_127468)

Species Accession Gene Product
Arabidopsis thaliana AT3G55400   methionyl-tRNA synthetase
Babesia bovis BBOV_I001970   methionyl-tRNA synthetase, putative
Brugia malayi Bm1_54415   methionyl-tRNA synthetase
Candida albicans CaO19.3950   mitochondrial tRNA methionyl-tRNA synthetase similar to S. cerevisiae MSM1 (YGR171C) mitochondrial methionyl-tRNA synthetase
Candida albicans CaO19.11432   mitochondrial tRNA methionyl-tRNA synthetase similar to S. cerevisiae MSM1 (YGR171C) mitochondrial methionyl-tRNA synthetase
Caenorhabditis elegans CELE_Y105E8A.20   Protein Y105E8A.20, isoform A
Cryptosporidium hominis Chro.80398   methionine -- tRNA ligase
Cryptosporidium parvum cgd8_3460   methionyl-tRNA synthetase of possible bacterial origin
Dictyostelium discoideum DDB_G0285759   methionine-tRNA ligase
Drosophila melanogaster Dmel_CG31322   Methionyl-tRNA synthetase
Echinococcus granulosus EgrG_000186800   methionine tRNA synthetase
Echinococcus multilocularis EmuJ_000186800   methionine tRNA synthetase
Giardia lamblia GL50803_22204   Methionyl-tRNA synthetase
Homo sapiens ENSG00000247626   methionyl-tRNA synthetase 2, mitochondrial
Leishmania braziliensis LbrM.21.0900   methionyl-tRNA synthetase, putative
Leishmania donovani LdBPK_210890.1   methionyl-tRNA synthetase, putative
Leishmania infantum LinJ.21.0890   methionyl-tRNA synthetase, putative
Leishmania major LmjF.21.0810   methionyl-tRNA synthetase, putative
Leishmania mexicana LmxM.21.0810   methionyl-tRNA synthetase, putative
Loa Loa (eye worm) LOAG_10885   tyrosyl-tRNA synthetase
Loa Loa (eye worm) LOAG_02240   methionyl-tRNA synthetase
Mycobacterium leprae ML0238c   Probable methionyl-tRNA synthase MetS
Mus musculus 212679   methionine-tRNA synthetase 2 (mitochondrial)
Mycobacterium tuberculosis Rv1007c   Methionyl-tRNA synthetase MetS (MetRS) (methionine--tRNA ligase)
Mycobacterium ulcerans MUL_4654   methionyl-tRNA synthetase
Neospora caninum NCLIV_041650   Methionine--tRNA ligase (EC 6.1.1.10), related
Oryza sativa 4332018   Os03g0209600
Onchocerca volvulus OVOC12840  
Plasmodium berghei PBANKA_0518700   methionine--tRNA ligase, putative
Plasmodium falciparum PF3D7_1034900   methionine--tRNA ligase
Plasmodium knowlesi PKNH_0620100   methionine--tRNA ligase, putative
Plasmodium vivax PVX_110980   methionine--tRNA ligase, putative
Plasmodium yoelii PY03894   methionyl-tRNA synthetase
Saccharomyces cerevisiae YGR171C   methionine--tRNA ligase MSM1
Schistosoma japonicum Sjp_0206550   ko:K01874 methionyl-tRNA synthetase [EC6.1.1.10], putative
Schistosoma mansoni Smp_005330   methionine-tRNA synthetase
Schmidtea mediterranea mk4.010622.00  
Schmidtea mediterranea mk4.019340.01  
Schmidtea mediterranea mk4.016299.00   MethionineALQ-tRNA ligase, mitochondrial
Schmidtea mediterranea mk4.031319.00   MethionineALQ-tRNA ligase, mitochondrial
Trypanosoma brucei gambiense Tbg972.10.1750   methionyl-tRNA synthetase, putative
Trypanosoma brucei Tb927.10.1500   methionyl-tRNA synthetase, putative
Trypanosoma congolense TcIL3000_10_1300   methionyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.509247.50   methionyl-tRNA synthetase, putative
Toxoplasma gondii TGME49_289300   methionyl-tRNA synthetase
Theileria parva TP01_1212   methionyl-tRNA synthetase, putative
Theileria parva TP03_0137   methionyl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_266630   methionine-tRNA synthetase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0196   methionyl-tRNA synthetase

Essentiality

TGME49_289300 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1023 Mycobacterium tuberculosis essential nmpdr
Tb927.10.1500 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.1500 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.1500 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.1500 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y105E8A.20 Caenorhabditis elegans embryonic lethal wormbase
TGME49_289300 this record Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.

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
Staphylococcus aureus subsp. aureus MW2 Methionyl-tRNA synthetase Compounds References
Trypanosoma brucei methionyl-tRNA synthetase, putative Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) Methionyl-tRNA synthetase 682 aa 25.4% 684 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0066 0.2793 1
0.0229 0.366 1
0.0057 0.269 1
0.0063 0.3315 0.764
0.0406 0.2744 1
0.0123 0.3604 1
0.006 0.3565 0.7574
0.0291 0.3129 1
0.0066 0.4543 1
0.0263 0.3658 1
0.0066 1 1
0.0458 0.4264 1
0.0078 0.4068 0
0.0066 0.2954 1
0.0043 0.4732 1
0.0084 0.2975 1
0.0059 0.3533 1
0.0062 1 0.5
0.0264 0.3693 1
0.0395 0.4382 1
0.0094 0.4118 0
0.0093 0.2505 0.5972
0.0077 0.3255 1
0.0066 0.3784 1
0.0066 0.3754 1
0.0267 0.2601 1
0.0063 0.3315 0.764
0.0066 0.3754 1
0.0228 0.2578 1
0.04 0.3878 1
0.0066 0.3397 1
0.0066 0.3372 1
0.0066 1 0.5
0.0066 1 1
0.0147 0.4261 1
0.0066 1 1
0.0057 0.269 1
0.0081 0.4217 1
0.0066 0.3784 1
0.0066 0.3784 1
0.0062 1 1
0.0054 0.6868 0.9594
0.0066 0.8556 0.8556
0.0066 0.4211 1
0.0127 1 1
0.0066 1 0.5
0.0066 1 0.5
0.0453 0.3976 1
0.006 1 0.5
0.0046 0.4213 0.5
0.0066 1 0.5
0.0057 1 0.5
0.0471 0.3286 1
0.0066 0.5 0.5
0.0355 0.4047 1
0.0066 0.8402 1
0.0154 0.4261 1
0.0066 1 0.5
0.012 0.2932 1
0.0066 0.715 0.5
0.0561 0.2958 1
0.0066 0.2527 1
0.0107 0.2638 1
0.0276 0.3174 1
0.0062 1 0.5
0.0066 0.3455 1
0.0286 0.3697 1
0.0053 0.4211 1
0.0057 0.269 1

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.

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Gene identifier TGME49_289300 (Toxoplasma gondii), methionyl-tRNA synthetase
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