Detailed view for PF3D7_0925300

Basic information

TDR Targets ID: 4927
Plasmodium falciparum, proline--tRNA ligase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.78 | Length (AA): 579 | MW (Da): 68466 | 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

PF00587   tRNA synthetase class II core domain (G, H, P, S and T)

Gene Ontology

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

Structural information

Modbase 3D models:

There are 9 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
17 363 1ses (A) 83 411 17.00 0 0.98 0.69 0.05
75 546 1nj8 (A) 2 455 22.00 0 1 1.06 -0.27
75 557 1nj8 (A) 2 444 21.00 0 1 0.98 0.14
75 546 1nj8 (A) 2 455 19.00 0.00000085 1 0.963699 0.35
82 383 2j3l (A) 24 490 40.00 0 1 0.239789 0.45
449 544 1wu7 (A) 323 419 14.00 0.018 0.28 0.357503 -0.48
75 544 1nj8 (A) 2 453 19.00 0.00000011 1 1.01584 0.02
82 383 2j3l (A) 24 490 40.00 0 1 0.236989 0.48
406 579 4uos (A) 1 184 16.00 0.079 0.24 0.429818 -0.69

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 - 32 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, early schizont, Oocyst, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile gametocyte, early trophozoite, late trophozoite, Ring, Male Gametocyte. PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Sporozoite. Zanghi G
Show/Hide expression data references
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • 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.

Orthologs

Ortholog group members (OG5_128299)

Species Accession Gene Product
Babesia bovis BBOV_III011010   tRNA synthetase class II core domain containing protein
Brugia malayi Bm1_53720   Met-10+ like-protein
Brugia malayi Bm1_47665   probable proline-trna synthetase - fission yeast, putative
Caenorhabditis elegans CELE_T27F6.5   Protein PARS-2, isoform D
Chlamydia trachomatis CT_393   proline--tRNA ligase
Dictyostelium discoideum DDB_G0276079   proline-tRNA ligase
Drosophila melanogaster Dmel_CG12186   Prolyl-tRNA synthetase
Escherichia coli b0194   prolyl-tRNA synthetase
Echinococcus granulosus EgrG_000461800   prolyl tRNA synthetase mitochondrial
Echinococcus multilocularis EmuJ_000461800   prolyl tRNA synthetase, mitochondrial
Homo sapiens ENSG00000162396   prolyl-tRNA synthetase 2, mitochondrial (putative)
Loa Loa (eye worm) LOAG_05904   hypothetical protein
Mus musculus ENSMUSG00000043572   prolyl-tRNA synthetase (mitochondrial)(putative)
Mycobacterium tuberculosis Rv2845c   Probable prolyl-tRNA synthetase ProS (proline--tRNA ligase) (PRORS) (global RNA synthesis factor) (proline translase)
Mycobacterium ulcerans MUL_2116   prolyl-tRNA synthetase
Plasmodium berghei PBANKA_0826100   proline--tRNA ligase, putative
Plasmodium falciparum PF3D7_0925300   proline--tRNA ligase, putative
Plasmodium knowlesi PKNH_0723200   proline--tRNA ligase, putative
Plasmodium vivax PVX_099680   proline--tRNA ligase, putative
Plasmodium yoelii PY00927   prolyl-tRNA synthetase-related
Saccharomyces cerevisiae YER087W   putative proline--tRNA ligase AIM10
Schistosoma japonicum Sjp_0306460   Probable prolyl-tRNA synthetase, mitochondrial precursor, putative
Schistosoma japonicum Sjp_0117790   ko:K01881 prolyl-tRNA synthetase [EC6.1.1.15], putative
Schistosoma mansoni Smp_025260   prolyl-tRNA synthetase
Schmidtea mediterranea mk4.000424.07  
Schmidtea mediterranea mk4.000424.06  
Schmidtea mediterranea mk4.000424.05  
Treponema pallidum TP0160   prolyl-tRNA synthetase
Theileria parva TP02_0040   prolyl-tRNA synthetase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0077   prolyl-tRNA synthetase

Essentiality

PF3D7_0925300 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b0194 Escherichia coli essential goodall
CELE_T27F6.5 Caenorhabditis elegans slow growth wormbase
Show/Hide essentiality data references
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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): 0.6

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
Candida albicans Prolyl-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
0.0223 0.8271 1
0.0306 0.2831 0.9077
0.0609 0.3141 1
0.0296 0.8381 1
0.0062 0.7136 0.5
0.0609 0.3141 1
0.0306 0.2831 0.9077
0.0613 0.8389 1
0.0125 0.7238 1
0.0306 0.2831 0.9077
0.01 0.4074 1
0.0264 0.3203 1
0.0302 0.3736 0.9299
0.03 0.8381 0.8674
0.0298 0.8362 1
0.0306 0.2831 0.9077
0.0038 0.6929 1
0.0203 0.8163 1
0.0258 0.8336 1
0.0187 0.454 1
0.0164 0.4901 0.4758
0.0288 0.831 0.8559
0.0201 0.8237 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_0925300 (Plasmodium falciparum), proline--tRNA ligase, putative
Title for this comment
Comment