Detailed view for PF3D7_1108200

Basic information

TDR Targets ID: 1572
Plasmodium falciparum, D-tyrosyl-tRNA(Tyr) deacylase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.8615 | Length (AA): 164 | MW (Da): 19205 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | 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

PF02580   D-Tyr-tRNA(Tyr) deacylase

Gene Ontology

Mouse over links to read term descriptions.
GO:0051499   D-aminoacyl-tRNA deacylase activity  
GO:0002161   GO:aminoacyl-tRNA editing activity  

GO:0005737   cytoplasm  
GO:0019478   D-amino acid catabolic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

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
1 156 1jke (A) 1 144 32.00 0 1 1.44 -1.57
1 160 2dbo (A) 1 148 43.00 0 1 1.55 -1.34
1 163 4nbi (A) 1 163 99.99 0 1 2.2774 -1.93

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
  • 3KNF:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3KNP:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3KO3:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3KO4:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3KO5:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3KO7:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3KO9:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3KOB:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3KOC:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3KOD:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3LMT:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3LMU:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3LMV:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4NBI:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4NBJ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5J61:
  • 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, Male Gametocyte. Otto TD Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs, Oocyst, Ring, Female Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 40 hs, late ring, Sporozoite. Otto TD PlasmoDB Zanghi G
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_127541)

Species Accession Gene Product
Arabidopsis thaliana AT4G18460   D-Tyr-tRNA(Tyr) deacylase family protein
Brugia malayi Bm1_04600   D-tyrosyl-tRNA(Tyr) deacylase
Candida albicans CaO19.297   D-Tyr-tRNA[Tyr] deacylase
Candida albicans CaO19.7911   D-Tyr-tRNA[Tyr] deacylase
Candida albicans CaO19.7929   D-Tyr-tRNA[Tyr] deacylase
Candida albicans CaO19.279   D-Tyr-tRNA[Tyr] deacylase
Caenorhabditis elegans CELE_T16G1.10   Protein PQN-68, isoform A
Cryptosporidium hominis Chro.70583   RNA helicase-like protein
Cryptosporidium parvum cgd7_5230   possible D-Tyr-tRNatyr deacylase
Dictyostelium discoideum DDB_G0291273   D-tyrosyl-tRNA deacylase
Drosophila melanogaster Dmel_CG18643   CG18643 gene product from transcript CG18643-RC
Escherichia coli b3887   D-tyr-tRNA(Tyr) deacylase
Echinococcus granulosus EgrG_000767800   hypothetical protein
Echinococcus granulosus EgrG_000767700   D tyrosyl tRNATyr deacylase
Entamoeba histolytica EHI_118150   D-tyrosyl-tRNA(Tyr) deacylase, putative
Echinococcus multilocularis EmuJ_000767700   D tyrosyl tRNA(Tyr) deacylase
Echinococcus multilocularis EmuJ_000767800   conserved hypothetical protein
Giardia lamblia GL50803_13832   D-tyrosyl-tRNA deacylase
Homo sapiens ENSG00000125821   D-tyrosyl-tRNA deacylase 1
Leishmania braziliensis LbrM.35.2950   D-tyrosyl-tRNA deacylase, putative
Leishmania donovani LdBPK_362870.1   D-tyrosyl-tRNA deacylase, putative
Leishmania infantum LinJ.36.2870   D-tyrosyl-tRNA deacylase, putative
Leishmania major LmjF.36.2730   D-tyrosyl-tRNA deacylase, putative
Leishmania mexicana LmxM.36.2730   D-tyrosyl-tRNA deacylase, putative
Loa Loa (eye worm) LOAG_06351   D-tyrosyl-tRNA deacylase
Mus musculus ENSMUSG00000027430   D-tyrosyl-tRNA deacylase 1
Mycobacterium tuberculosis Rv1897c   Conserved hypothetical protein
Mycobacterium ulcerans MUL_2960   D-tyrosyl-tRNA(Tyr) deacylase
Neospora caninum NCLIV_061570   D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-), related
Oryza sativa 4327697   Os01g0242500
Plasmodium berghei PBANKA_0938700   D-tyrosyl-tRNA(Tyr) deacylase, putative
Plasmodium falciparum PF3D7_1108200   D-tyrosyl-tRNA(Tyr) deacylase
Plasmodium knowlesi PKNH_0905800   D-tyrosyl-tRNA(Tyr) deacylase, putative
Plasmodium vivax PVX_091090   D-tyrosyl-tRNA(Tyr) deacylase, putative
Plasmodium yoelii PY00917   predicted using Genefinder
Saccharomyces cerevisiae YDL219W   Dtd1p
Schistosoma japonicum Sjp_0040420   ko:K01175 DTD1, C20orf88, HARS2; D-tyrosyl-tRNA deacylase 1 homolog [EC:3.1.-.-], putative
Schistosoma mansoni Smp_146570   histidyl-tRNA synthetase-related
Schmidtea mediterranea mk4.003187.01   D-tyrosyl-tRNA(Tyr) deacylase 1
Trypanosoma brucei gambiense Tbg972.10.8810   D-tyrosyl-tRNA deacylase, putative
Trypanosoma brucei Tb927.10.7190   D-tyrosyl-tRNA deacylase, putative
Trypanosoma congolense TcIL3000_10_6170   D-tyrosyl-tRNA deacylase, putative
Toxoplasma gondii TGME49_218810   histidyl-tRNA synthetase
Trichomonas vaginalis TVAG_010100   D-tyrosyl-tRNA(tyr) deacylase, putative

Essentiality

PF3D7_1108200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.7190 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.7190 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.7190 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.7190 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b3887 Escherichia coli non-essential goodall
TGME49_218810 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.

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Gene identifier PF3D7_1108200 (Plasmodium falciparum), D-tyrosyl-tRNA(Tyr) deacylase
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