Detailed view for PF3D7_1216000

Basic information

TDR Targets ID: 5204
Plasmodium falciparum, serine--tRNA ligase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.1409 | Length (AA): 618 | MW (Da): 73272 | Paralog Number: 1

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:0004828   serine-tRNA ligase activity  
GO:0004812   aminoacyl-tRNA ligase activity  
GO:0000166   nucleotide binding  
GO:0006434   seryl-tRNA aminoacylation  
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
99 615 1ses (A) 3 419 25.00 0 1 0.86 0.3
201 613 1wle (A) 76 473 26.00 0 1 0.97 -0.58
43 614 3err (A) 3 418 20.00 0 1 0.928066 0.83
46 265 4tql (A) 9 238 17.00 0.0000026 0.25 0.534787 -0.9
170 616 2dq3 (A) 1 425 37.00 0 1 1.0558 -0.08
13 95 2i1k (A) 349 441 7.00 0.1 0 0.167704 -0.07
43 614 3err (A) 3 418 22.00 0 1 0.993766 0.58
99 268 4uos (A) 1 180 24.00 0.00016 0.31 0.564381 -1.19
170 616 2dq3 (A) 1 425 37.00 0 1 1.0465 0.02

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 gametocyte, late trophozoite. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile 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, Ring, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, Oocyst, Sporozoite, Male Gametocyte. Otto TD Zanghi G Lasonder E
Show/Hide expression data references
  • 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
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_126677)

Species Accession Gene Product
Arabidopsis thaliana AT1G11870   Seryl-tRNA synthetase
Arabidopsis thaliana AT5G27470   seryl-tRNA synthetase / serine--tRNA ligase
Babesia bovis BBOV_IV001340   hypothetical protein
Babesia bovis BBOV_IV007240   seryl-tRNA synthetase, putative
Brugia malayi Bm1_41310   Sars1 protein
Brugia malayi Bm1_39760   seryl-tRNA synthetase, mitochondrial precursor, putative
Candida albicans CaO19.269   likely tRNA synthetase similar to S. cerevisiae SES1 (YDR023W) serine tRNA synthetase
Candida albicans CaO19.7901   likely tRNA synthetase similar to S. cerevisiae SES1 (YDR023W) serine tRNA synthetase
Candida albicans CaO19.8792   possible mitochondrial function
Candida albicans CaO19.1201   possible mitochondrial function
Caenorhabditis elegans CELE_C47E12.1   Protein SARS-1
Caenorhabditis elegans CELE_W03B1.4   Protein SARS-2
Cryptosporidium hominis Chro.80542   hypothetical protein
Cryptosporidium parvum cgd8_4720   seryl-tRNA synthetase, cytoplasmic
Chlamydia trachomatis CT_729   serine--tRNA ligase
Dictyostelium discoideum DDB_G0272660   serine-tRNA ligase
Dictyostelium discoideum DDB_G0267604   serine-tRNA ligase
Drosophila melanogaster Dmel_CG17259   CG17259 gene product from transcript CG17259-RA
Drosophila melanogaster Dmel_CG4938   Seryl-tRNA synthetase
Escherichia coli b0893   seryl-tRNA synthetase, also charges selenocysteinyl-tRNA with serine
Echinococcus granulosus EgrG_001197300   Seryl tRNA Synthetase
Echinococcus granulosus EgrG_000239900   seryl tRNA synthetase mitochondrial
Entamoeba histolytica EHI_092640   seryl-tRNA synthetase, putative
Entamoeba histolytica EHI_000690   seryl-tRNA synthetase, putative
Echinococcus multilocularis EmuJ_001197300   Seryl tRNA Synthetase
Echinococcus multilocularis EmuJ_000239900   seryl tRNA synthetase, mitochondrial
Giardia lamblia GL50803_101501   Seryl-tRNA synthetase
Homo sapiens ENSG00000031698   seryl-tRNA synthetase
Homo sapiens ENSG00000104835   seryl-tRNA synthetase 2, mitochondrial
Leishmania braziliensis LbrM.19.0220   seryl-tRNA synthetase, putative
Leishmania donovani LdBPK_110100.1   seryl-tRNA synthetase
Leishmania infantum LinJ.11.0100   seryl-tRNA synthetase, putative
Leishmania major LmjF.11.0100   seryl-tRNA synthetase, putative
Leishmania mexicana LmxM.11.0100   seryl-tRNA synthetase, putative
Loa Loa (eye worm) LOAG_00733   seryl-tRNA synthetase
Loa Loa (eye worm) LOAG_06820   Sars1 protein
Mycobacterium leprae ML0082   Probable seryl-tRNA synthetase SerS (serine--tRNA ligase) (SERRS) (serine translase)
Mus musculus ENSMUSG00000068739   seryl-aminoacyl-tRNA synthetase
Mus musculus ENSMUSG00000070699   seryl-aminoacyl-tRNA synthetase 2
Mycobacterium tuberculosis Rv3834c   SERYL-tRNA synthetase SerS (serine--tRNA ligase) (SERRS) (serine translase)
Mycobacterium ulcerans MUL_5006   seryl-tRNA synthetase
Neospora caninum NCLIV_066770   seryl-tRNA synthetase, putative
Oryza sativa 4350906   Os11g0610900
Oryza sativa 4324679   Os01g0559100
Oryza sativa 4331954   Os03g0198400
Plasmodium berghei PBANKA_0615400   serine--tRNA ligase, putative
Plasmodium berghei PBANKA_1431700   serine--tRNA ligase, putative
Plasmodium falciparum PF3D7_1216000   serine--tRNA ligase, putative
Plasmodium falciparum PF3D7_0717700   serine--tRNA ligase, putative
Plasmodium knowlesi PKNH_0312700   serine--tRNA ligase, putative
Plasmodium knowlesi PKNH_1435500   serine--tRNA ligase, putative
Plasmodium vivax PVX_000545   serine--tRNA ligase, putative
Plasmodium vivax PVX_123480   serine--tRNA ligase, putative
Plasmodium yoelii PY03295   seryl-tRNA synthetase
Saccharomyces cerevisiae YDR023W   serine--tRNA ligase SES1
Saccharomyces cerevisiae YHR011W   putative serine--tRNA ligase DIA4
Schistosoma japonicum Sjp_0300880   ko:K01875 seryl-tRNA synthetase [EC6.1.1.11], putative
Schistosoma japonicum Sjp_0075820   ko:K01875 seryl-tRNA synthetase [EC6.1.1.11], putative
Schistosoma mansoni Smp_053610   seryl-tRNA synthetase
Schistosoma mansoni Smp_057230   seryl-tRNA synthetase
Schmidtea mediterranea mk4.029516.01  
Schmidtea mediterranea mk4.016422.00  
Schmidtea mediterranea mk4.006981.00  
Schmidtea mediterranea mk4.012585.01  
Schmidtea mediterranea mk4.000337.18   Probable serineALQ-tRNA ligase, cytoplasmic
Trypanosoma brucei gambiense Tbg972.11.8110   seryl-tRNA synthetase, putative
Trypanosoma brucei Tb927.11.7170   seryl-tRNA synthetase
Trypanosoma congolense TcIL3000.11.7740   seryl-tRNA synthetase
Trypanosoma cruzi TcCLB.506777.80   seryl-tRNA synthetase
Toxoplasma gondii TGME49_251690   seryl-tRNA synthetase, cytoplasmic, putative
Treponema pallidum TP0647   seryl-tRNA synthetase
Theileria parva TP01_0161   seryl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_305400   seryl-tRNA synthetase, putative
Trichomonas vaginalis TVAG_101870   seryl-tRNA synthetase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0464   seryl-tRNA synthetase

Essentiality

PF3D7_1216000 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.5020 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.5020 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.5020 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.02.5020 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b0893 Escherichia coli essential goodall
CELE_W03B1.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_W03B1.4 Caenorhabditis elegans larval arrest wormbase
CELE_W03B1.4 Caenorhabditis elegans slow growth wormbase
CELE_C47E12.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_C47E12.1 Caenorhabditis elegans larval arrest wormbase
CELE_C47E12.1 Caenorhabditis elegans slow growth wormbase
YDR023W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0615400 Plasmodium berghei Dispensable plasmo
PBANKA_1431700 Plasmodium berghei Essential plasmo
TGME49_251690 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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

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_1216000 (Plasmodium falciparum), serine--tRNA ligase, putative
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