Detailed view for PF3D7_1349200

Basic information

TDR Targets ID: 2236
Plasmodium falciparum, glutamate--tRNA ligase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.0563 | Length (AA): 863 | MW (Da): 101418 | Paralog Number: 0

Signal peptide: N | 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

PF00749   tRNA synthetases class I (E and Q), catalytic domain
PF03950   tRNA synthetases class I (E and Q), anti-codon binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0005524   ATP binding  
GO:0004818   glutamate-tRNA ligase activity  
GO:0004812   aminoacyl-tRNA ligase activity  
GO:0000166   nucleotide binding  
GO:0006424   glutamyl-tRNA aminoacylation  
GO:0006418   tRNA aminoacylation for protein translation  
GO:0006412   translation  
GO:0043039   tRNA aminoacylation  

Structural information

Modbase 3D models:

There are 18 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
22 252 1axd (A) 4 207 12.00 0 0.1 0.19 -0.15
292 809 1qtq (A) 8 540 36.00 0 1 1.06 -0.71
311 555 1j09 (A) 2 256 32.00 0.0000000014 1 0.39 0.65
6 117 3hn6 (A) 23 131 33.00 0.4 0.09 0.18218 0.47
75 249 1aw9 (A) 10 205 13.00 0.63 0.84 0.292381 -0.41
278 826 4r3z (C) 231 771 28.00 0 1 0.830753 0.9
304 797 4p2b (A) 31 550 35.00 0 1 0.908822 0.34
308 822 4jxx (A) 24 548 36.00 0 1 0.990355 0.01
315 814 5bnz (A) 33 550 34.00 0 1 0.960974 -0.07
808 858 1llm (C) 104 154 8.00 0.033 0 0.311996 -1.98
19 217 2r4g (A) 285 491 30.00 0.15 0.06 0.238811 0.97
69 128 1aw9 (A) 3 57 7.00 0.066 0 0.143807 -1.11
284 820 4r3z (C) 231 769 28.00 0 1 0.847826 0.72
301 806 2hz7 (A) 52 609 32.00 0 1 0.887875 0.24
310 803 4p2b (A) 31 550 35.00 0 1 0.904114 0.34
314 823 4jxx (A) 24 548 36.00 0 1 1.00086 -0.12
837 872 2ytd (A) 8 41 15.00 0.0098 0.02 0.437384 -3.25
838 872 2ytt (A) 9 41 18.00 0.014 0.02 0.486238 -3.55

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 intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late trophozoite, Oocyst, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, late schizont, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% 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.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB

Orthologs

Ortholog group members (OG5_128638)

Species Accession Gene Product
Arabidopsis thaliana AT5G26710   glutamyl/glutaminyl-tRNA synthetase, class Ic
Babesia bovis BBOV_III011840   glutamyl-tRNA synthetase family protein
Candida albicans CaO19_7057   hypothetical protein
Candida albicans CaO19.7057   similar to S. cerevisiae YGL245W
Caenorhabditis elegans CELE_ZC434.5   Protein EARS-1
Cryptosporidium hominis Chro.80098   glutamate--tRNA ligase
Cryptosporidium parvum cgd8_790   glutamate--tRNA ligase
Dictyostelium discoideum DDB_G0287467   glutamate-tRNA ligase
Entamoeba histolytica EHI_155570   glutamyl-tRNA synthetase, putative
Giardia lamblia GL50803_86681   Glutaminyl-tRNA synthetase
Leishmania braziliensis LbrM.30.3280   glutamyl-tRNA synthetase, putative
Leishmania donovani LdBPK_303290.1   glutamyl-tRNA synthetase, putative
Leishmania infantum LinJ.30.3290   glutamyl-tRNA synthetase, putative
Leishmania major LmjF.30.3240   glutamyl-tRNA synthetase, putative
Leishmania mexicana LmxM.29.3240   glutamyl-tRNA synthetase, putative
Neospora caninum NCLIV_024090   glutamyl-tRNA synthetase, putative
Oryza sativa 4348464   Os10g0369000
Oryza sativa 4325167   Os01g0271200
Plasmodium berghei PBANKA_1362000   glutamate--tRNA ligase, putative
Plasmodium falciparum PF3D7_1349200   glutamate--tRNA ligase, putative
Plasmodium knowlesi PKNH_1251700   glutamate--tRNA ligase, putative
Plasmodium vivax PVX_083355   glutamate--tRNA ligase, putative
Plasmodium yoelii PY02891   glutamyl-tRNA synthetase, putative
Saccharomyces cerevisiae YGL245W   glutamate--tRNA ligase GUS1
Trypanosoma brucei gambiense Tbg972.6.4410   glutamyl-tRNA synthetase, putative
Trypanosoma brucei Tb11.v5.0810   glutamyl-tRNA synthetase, putative
Trypanosoma brucei Tb927.6.4590   glutamyl-tRNA synthetase, putative
Trypanosoma congolense TcIL3000_6_4040   glutamyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.511731.60   glutamyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.506831.70   glutamyl-tRNA synthetase, putative
Toxoplasma gondii TGME49_263870   glutamate-tRNA ligase
Theileria parva TP01_1053   glutamyl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_047990   glutaminyl-tRNA synthetase, putative

Essentiality

PF3D7_1349200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.4590 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.6.4590 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.6.4590 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.6.4590 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_ZC434.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_ZC434.5 Caenorhabditis elegans larval lethal wormbase
CELE_ZC434.5 Caenorhabditis elegans slow growth wormbase
YGL245W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1362000 Plasmodium berghei Essential plasmo
TGME49_263870 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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): 0.3

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

  • Assay for Aminoacyl-tRNA Synthetase (6.1.1.17 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

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.

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Gene identifier PF3D7_1349200 (Plasmodium falciparum), glutamate--tRNA ligase, putative
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