Detailed view for PVX_002940

Basic information

TDR Targets ID: 267953
Plasmodium vivax, asparagine--tRNA ligase, putative
Source Database / ID:  PlasmoDB 

pI: 6.5646 | Length (AA): 584 | MW (Da): 66338 | Paralog Number: 1

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

Druggability Group : DG5

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

PF00152   tRNA synthetases class II (D, K and N)
PF01336   OB-fold nucleic acid binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0004812   aminoacyl-tRNA ligase activity  
GO:0004601   peroxidase activity  
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  
GO:0020037   heme binding  
GO:0005524   ATP binding  
GO:0004816   asparagine-tRNA ligase activity  
GO:0004815   aspartate-tRNA ligase activity  
GO:0055114   oxidation reduction  
GO:0006979   response to oxidative stress  
GO:0006422   aspartyl-tRNA aminoacylation  
GO:0006421   asparaginyl-tRNA aminoacylation  
GO:0006418   tRNA aminoacylation for protein translation  
GO:0006412   translation  

Metabolic Pathways

Aminoacyl-tRNA biosynthesis (KEGG)

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
24 580 1e1o (A) 12 502 19.00 0 1 0.76 1.05
76 579 1x54 (A) 11 429 35.00 0 1 1.07 0.01
31 576 1bbu (A) 13 498 20.00 0 1 0.855232 1.49
66 582 1x54 (A) 1 432 31.00 0 1 1.01857 0.66
305 579 1eov (A) 277 552 29.00 0 1 0.64209 1.08
454 581 4ah6 (A) 496 611 37.00 0.0000022 0.3 0.276378 1.62

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
Upper 80-100% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intraerythrocytic - 30 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intraerythrocytic - 36 hs, intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Show/Hide expression data references
  • Zhu L New insights into the Plasmodium vivax transcriptome using RNA-Seq.

Orthologs

Ortholog group members (OG5_126756)

Species Accession Gene Product
Arabidopsis thaliana AT4G17300   asparaginyl-tRNA synthetase
Arabidopsis thaliana AT1G70980   asparagine--tRNA ligase
Arabidopsis thaliana AT5G56680   asparaginyl-tRNA synthetase, cytoplasmic 1
Babesia bovis BBOV_IV009530   asparaginyl-tRNA synthetase, putative
Babesia bovis BBOV_III011270   asparaginyl-tRNA synthetase family protein
Brugia malayi Bm1_36235   Asparaginyl-tRNA synthetase, cytoplasmic
Brugia malayi Bm1_52355   60K filarial antigen - nematode
Brugia malayi Bm1_55920   Asparaginyl-tRNA synthetase
Candida albicans CaO19.13990   similar to S. cerevisiae YCR024C
Candida albicans CaO19.6698   similar to S. cerevisiae YCR024C
Candida albicans CaO19.13994   asparaginyl-tRNA synthetase
Candida albicans CaO19_6698   hypothetical protein
Candida albicans CaO19_6702   hypothetical protein
Candida albicans CaO19.6702   asparaginyl-tRNA synthetase
Caenorhabditis elegans CELE_Y66D12A.23   Protein NARS-2
Caenorhabditis elegans CELE_F22D6.3   Protein NARS-1, isoform A
Cryptosporidium hominis Chro.80047   asparaginyl-tRNA synthetase
Cryptosporidium parvum cgd8_350   asparaginyl-tRNA synthetase (NOB+tRNA synthase)
Dictyostelium discoideum DDB_G0268100   asparagine-tRNA ligase
Dictyostelium discoideum DDB_G0275263   asparagine-tRNA ligase
Drosophila melanogaster Dmel_CG6796   CG6796 gene product from transcript CG6796-RA
Drosophila melanogaster Dmel_CG10687   Asparaginyl-tRNA synthetase
Escherichia coli b0930   asparaginyl tRNA synthetase
Echinococcus granulosus EgrG_002026800   asparaginyl tRNA synthetase, cytoplasmic
Echinococcus granulosus EgrG_000889700   asparaginyl tRNA synthetase
Echinococcus granulosus EgrG_000348600   asparaginyl tRNA synthetase cytoplasmic
Entamoeba histolytica EHI_126920   asparaginyl-tRNA synthetase, putative
Echinococcus multilocularis EmuJ_000348700   asparaginyl tRNA synthetase
Echinococcus multilocularis EmuJ_000348300   asparaginyl tRNA synthetase, cytoplasmic
Echinococcus multilocularis EmuJ_000889700   asparaginyl tRNA synthetase
Echinococcus multilocularis EmuJ_000348600   asparaginyl tRNA synthetase, cytoplasmic
Giardia lamblia GL50803_14375   Asparaginyl-tRNA synthetase
Homo sapiens ENSG00000137513   asparaginyl-tRNA synthetase 2, mitochondrial (putative)
Homo sapiens ENSG00000134440   asparaginyl-tRNA synthetase
Leishmania braziliensis LbrM.20.1840   asparaginyl-tRNA synthetase, putative
Leishmania donovani LdBPK_342110.1   asparaginyl-tRNA synthetase, putative
Leishmania infantum LinJ.34.2110   asparaginyl-tRNA synthetase, putative
Leishmania major LmjF.34.2340   asparaginyl-tRNA synthetase, putative
Leishmania mexicana LmxM.33.2340   asparaginyl-tRNA synthetase, putative
Loa Loa (eye worm) LOAG_08758   hypothetical protein
Loa Loa (eye worm) LOAG_08301   63kd antigen
Mus musculus ENSMUSG00000024587   asparaginyl-tRNA synthetase
Mus musculus ENSMUSG00000018995   asparaginyl-tRNA synthetase 2 (mitochondrial)(putative)
Neospora caninum NCLIV_036250   Asparaginyl-tRNA synthetase, related
Oryza sativa 4325717   Os01g0372700
Oryza sativa 4343250   Os07g0485400
Plasmodium berghei PBANKA_1109200   asparagine--tRNA ligase, putative
Plasmodium berghei PBANKA_0308600   asparagine--tRNA ligase, putative
Plasmodium falciparum PF3D7_0509600   asparagine--tRNA ligase
Plasmodium falciparum PF3D7_0211800   asparagine--tRNA ligase
Plasmodium knowlesi PKNH_0409400   asparagine--tRNA ligase, putative
Plasmodium knowlesi PKNH_1024000   asparagine--tRNA ligase, putative
Plasmodium vivax PVX_098040   asparagine--tRNA ligase, putative
Plasmodium vivax PVX_002940   asparagine--tRNA ligase, putative
Plasmodium yoelii PY05639   asparaginyl-tRNA synthetase
Plasmodium yoelii PY02504   asparaginyl-tRNA synthetase
Plasmodium yoelii PY03253   asparaginyl-tRNA synthetase
Saccharomyces cerevisiae YHR019C   asparagine--tRNA ligase DED81
Saccharomyces cerevisiae YCR024C   asparagine--tRNA ligase SLM5
Schistosoma japonicum Sjp_0209560   ko:K01893 asparaginyl-tRNA synthetase [EC6.1.1.22], putative
Schistosoma japonicum Sjp_0121910   IPR004365,nucleic acid binding, OB-fold, tRNA/helicase-type;IPR008994,Nucleic acid-binding, OB-fold,domain-containing
Schistosoma mansoni Smp_169030   aspartyl-tRNA synthetase
Schistosoma mansoni Smp_041450   aspartyl-tRNA synthetase
Schmidtea mediterranea mk4.042846.03   AsparagineALQ-tRNA ligase, cytoplasmic
Schmidtea mediterranea mk4.000202.11   Aspartyl-tRNA synthetase, putative
Schmidtea mediterranea mk4.000143.03  
Trypanosoma brucei gambiense Tbg972.4.2280   asparaginyl-tRNA synthetase, putative
Trypanosoma brucei Tb927.4.2310   asparaginyl-tRNA synthetase, putative
Trypanosoma congolense TcIL3000_4_2130   asparaginyl-tRNA synthetase, putative
Trypanosoma cruzi TcCLB.506559.350   asparaginyl-tRNA synthetase, putative
Toxoplasma gondii TGME49_270510   asparaginyl-tRNA synthetase (NOB+tRNA synthase)
Treponema pallidum TP0609   asparaginyl-tRNA synthetase
Theileria parva TP01_0818   asparaginyl-tRNA synthetase, putative
Theileria parva TP02_0746   asparaginyl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_156640   aspartyl/lysyl-tRNA synthetase, putative

Essentiality

PVX_002940 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.2310 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.4.2310 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.4.2310 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.4.2310 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b0930 Escherichia coli essential goodall
CELE_F22D6.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_F22D6.3 Caenorhabditis elegans larval arrest wormbase
CELE_F22D6.3 Caenorhabditis elegans sterile wormbase
YHR019C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0308600 Plasmodium berghei Slow plasmo
PBANKA_1109200 Plasmodium berghei Essential plasmo
TGME49_270510 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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.
  • 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
  • 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.
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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

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 PVX_002940 (Plasmodium vivax), asparagine--tRNA ligase, putative
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