Detailed view for PF3D7_1117500

Basic information

TDR Targets ID: 1650
Plasmodium falciparum, tyrosine--tRNA ligase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.2781 | Length (AA): 561 | MW (Da): 66419 | Paralog Number: 0

Signal peptide: Y | GPI Anchor: N | 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

PF00579   tRNA synthetases class I (W and Y)

Gene Ontology

Mouse over links to read term descriptions.
GO:0020011   apicoplast  
GO:0005737   cytoplasm  
GO:0005524   ATP binding  
GO:0004831   tyrosine-tRNA ligase activity  
GO:0004812   aminoacyl-tRNA ligase activity  
GO:0003723   RNA binding  
GO:0000166   nucleotide binding  
GO:0006437   tyrosyl-tRNA aminoacylation  
GO:0006418   tRNA aminoacylation for protein translation  
GO:0006412   translation  

Structural information

Modbase 3D models:

There are 6 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
25 462 1y42 (X) 42 419 22.00 0 1 0.51 0.38
44 428 2cyb (A) 2 319 17.00 0 0.65 0.38 -0.04
47 366 1wq3 (A) 4 288 32.00 0 1 0.86 -0.95
52 562 1h3f (A) 13 432 18.00 0 1 0.64 0.31
47 561 4oud (A) 4 424 28.00 0 1 0.885304 0.55
482 558 1jh3 (A) 23 96 22.00 0.00000013 0.99 0.465155 -0.62

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
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, late trophozoite, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, early trophozoite, Oocyst, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Female Gametocyte, Male Gametocyte. Lasonder E
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.

Orthologs

Ortholog group members (OG5_127413)

Species Accession Gene Product
Arabidopsis thaliana AT3G02660   tyrosyl-tRNA synthetase
Babesia bovis BBOV_IV010950   tyrosyl-tRNA synthetase, putative
Brugia malayi Bm1_36385   tyrosyl-tRNA synthetase family protein
Candida albicans CaO19.7756   likely tRNA synthetase similar to S. cerevisiae MSY1 (YPL097W) mitochondrial tyrosyl-tRNA synthetase
Candida albicans CaO19.109   likely tRNA synthetase similar to S. cerevisiae MSY1 (YPL097W) mitochondrial tyrosyl-tRNA synthetase
Caenorhabditis elegans CELE_K08F11.4   Protein YARS-1, isoform B
Chlamydia trachomatis CT_062   tyrosine--tRNA ligase
Dictyostelium discoideum DDB_G0279715   tyrosine-tRNA ligase
Drosophila melanogaster Dmel_CG16912   mitochondrial tyrosyl-tRNA synthetase
Escherichia coli b1637   tyrosyl-tRNA synthetase
Echinococcus granulosus EgrG_000901500   tyrosyl tRNA synthetase
Echinococcus multilocularis EmuJ_000901500   tyrosyl tRNA synthetase
Homo sapiens ENSG00000139131   tyrosyl-tRNA synthetase 2, mitochondrial
Loa Loa (eye worm) LOAG_04233   tyrosyl-tRNA synthetase
Mycobacterium leprae ML1352   Probable Tyrosyl-tRNA synthase TyrS (TYRRS)
Mus musculus ENSMUSG00000022792   tyrosyl-tRNA synthetase 2 (mitochondrial)
Mycobacterium tuberculosis Rv1689   Probable tyrosyl-tRNA synthase TyrS (TYRRS)
Mycobacterium ulcerans MUL_1668   tyrosyl-tRNA synthetase
Neospora caninum NCLIV_034220   tyrosyl-tRNA synthetase, putative
Oryza sativa 4324476   Os01g0500900
Plasmodium berghei PBANKA_0930500   tyrosine--tRNA ligase, putative
Plasmodium falciparum PF3D7_1117500   tyrosine--tRNA ligase
Plasmodium knowlesi PKNH_0915200   tyrosine--tRNA ligase, putative
Plasmodium vivax PVX_091505   tyrosine--tRNA ligase, putative
Plasmodium yoelii PY06291   Tyrosyl-tRNA synthetase
Plasmodium yoelii PY04254   tyrosyl-tRNA synthetase 1-related
Saccharomyces cerevisiae YPL097W   tyrosine--tRNA ligase MSY1
Schistosoma japonicum Sjp_0072860   ko:K01866 tyrosyl-tRNA synthetase [EC6.1.1.1], putative
Schistosoma mansoni Smp_176290   tyrosyl-tRNA synthetase
Schmidtea mediterranea mk4.000439.03  
Toxoplasma gondii TGME49_273410   tyrosine-tRNA ligase
Treponema pallidum TP0834   tyrosyl-tRNA synthetase (tyrS)
Theileria parva TP01_0760   tyrosyl-tRNA synthetase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0248   tyrosyl-tRNA synthetase

Essentiality

PF3D7_1117500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu1718 Mycobacterium tuberculosis essential nmpdr
b1637 Escherichia coli essential goodall
CELE_K08F11.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_K08F11.4 Caenorhabditis elegans larval arrest wormbase
CELE_K08F11.4 Caenorhabditis elegans slow growth wormbase
CELE_K08F11.4 Caenorhabditis elegans sterile wormbase
TGME49_273410 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.

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): 0.1

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.

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Gene identifier PF3D7_1117500 (Plasmodium falciparum), tyrosine--tRNA ligase
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