Detailed view for PF3D7_0807900

Basic information

TDR Targets ID: 642
Plasmodium falciparum, tyrosine--tRNA ligase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.5012 | Length (AA): 373 | MW (Da): 43453 | Paralog Number: 0

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

Druggability Group : DG3

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:0000166   nucleotide binding  
GO:0005524   ATP binding  
GO:0004831   tyrosine-tRNA ligase activity  
GO:0004812   aminoacyl-tRNA ligase activity  
GO:0006437   tyrosyl-tRNA aminoacylation  
GO:0006418   tRNA aminoacylation for protein translation  
GO:0006412   translation  

Structural information

Modbase 3D models:

There are 5 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
2 372 1r6u (A) 83 462 20.00 0 1 1.09 0.21
26 366 2cyc (A) 2 371 36.00 0 1 1.34 -1.39
26 367 2cya (A) 5 359 35.00 0 1 1.44 -1.31
20 372 3vgj (A) 20 372 99.99 0 1 2.20478 -1.72
20 372 3vgj (A) 20 372 99.99 0 1 2.20498 -1.71

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
  • 3VGJ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Oocyst, Ring, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile gametocyte, merozoite, Female Gametocyte, Male Gametocyte. PlasmoDB 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.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • 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_127567)

Species Accession Gene Product
Arabidopsis thaliana AT2G33840   tyrosyl-tRNA synthetase
Arabidopsis thaliana AT1G28350   probably tyrosine-tRNA synthetase
Babesia bovis BBOV_II002250   tyrosyl-tRNA synthetase, putative
Candida albicans CaO19.10209   tyrosyl-tRNA synthetase, cytoplasmic
Candida albicans CaO19.2694   tyrosyl-tRNA synthetase, cytoplasmic
Caenorhabditis elegans CELE_Y105E8A.19   Protein Y105E8A.19
Cryptosporidium hominis Chro.60344   tyrosyl-tRNA synthetase
Cryptosporidium parvum cgd6_2970   tyrosyl-tRNA synthetase (tyrosyl-tRNA ligase; TyrRS). class-I aaRS
Dictyostelium discoideum DDB_G0276721   tyrosine-tRNA ligase
Drosophila melanogaster Dmel_CG4561   Tyrosyl-tRNA synthetase
Echinococcus granulosus EgrG_001147800   tyrosyl tRNA synthetase
Entamoeba histolytica EHI_009240   tyrosyl-tRNA synthetase, putative
Echinococcus multilocularis EmuJ_001147800   tyrosyl tRNA synthetase
Giardia lamblia GL50803_16612   Tyrosyl-tRNA synthetase
Homo sapiens ENSG00000134684   tyrosyl-tRNA synthetase
Leishmania braziliensis LbrM.14.1560   tyrosyl-tRNA synthetase, putative
Leishmania donovani LdBPK_141460.1   tyrosyl-tRNA synthetase, putative
Leishmania infantum LinJ.14.1460   tyrosyl-tRNA synthetase, putative
Leishmania major LmjF.14.1370   tyrosyl-tRNA synthetase, putative
Leishmania mexicana LmxM.14.1370   tyrosyl-tRNA synthetase, putative
Mus musculus ENSMUSG00000028811   tyrosyl-tRNA synthetase
Neospora caninum NCLIV_066920   hypothetical protein
Oryza sativa 9271247   Os08g0320000
Oryza sativa 4344663   Os08g0150800
Plasmodium berghei PBANKA_1222800   tyrosine--tRNA ligase, putative
Plasmodium falciparum PF3D7_0807900   tyrosine--tRNA ligase
Plasmodium knowlesi PKNH_0110800   tyrosine--tRNA ligase, putative
Plasmodium vivax PVX_088145   tyrosine--tRNA ligase, putative
Plasmodium yoelii PY04194   tyrosyl-tRNA synthetase
Saccharomyces cerevisiae YGR185C   tyrosine--tRNA ligase TYS1
Schistosoma japonicum Sjp_0133030   ko:K01866 tyrosyl-tRNA synthetase [EC6.1.1.1], putative
Schistosoma japonicum Sjp_0047670   ko:K01866 tyrosyl-tRNA synthetase [EC6.1.1.1], putative
Schistosoma mansoni Smp_129210   tyrosyl-tRNA synthetase
Schmidtea mediterranea mk4.005516.00  
Schmidtea mediterranea mk4.007291.00   TyrosineALQ-tRNA ligase, cytoplasmic
Schmidtea mediterranea mk4.016312.01   TyrosineALQ-tRNA ligase, cytoplasmic
Trypanosoma brucei gambiense Tbg972.7.4020   tyrosyl-tRNA synthetase, putative
Trypanosoma brucei Tb927.7.3620   tyrosyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.509937.180   tyrosyl-tRNA synthetase, putative
Toxoplasma gondii TGME49_251880   tRNA synthetases class I family protein
Theileria parva TP04_0367   tyrosyl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_263250   isoleucyl, leucyl, tyrosyl, valyl and methionyl-tRNA synthetases, putative

Essentiality

PF3D7_0807900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.7.3620 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.3620 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.3620 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.7.3620 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y105E8A.19 Caenorhabditis elegans embryonic lethal wormbase
YGR185C Saccharomyces cerevisiae inviable yeastgenome
TGME49_251880 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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

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): 0.6

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 tyrosyl-tRNA synthetase Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0042 0.3692 1
0.005 0.3056 1
0.005 0.3056 1
0.0121 0.5444 1
0.0023 0.3761 1
0.0054 0.2547 1
0.0101 0.5406 1
0.0119 0.4195 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.

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

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier PF3D7_0807900 (Plasmodium falciparum), tyrosine--tRNA ligase
Title for this comment
Comment