Detailed view for PF3D7_1203500

Basic information

TDR Targets ID: 5083
Plasmodium falciparum, threonylcarbamoyl-AMP synthase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 5.5022 | Length (AA): 556 | MW (Da): 64888 | 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

PF01300   Telomere recombination
PF03481   Putative GTP-binding controlling metal-binding

Gene Ontology

Mouse over links to read term descriptions.
GO:0008150   biological_process  
GO:0005575   cellular_component  
GO:0003674   molecular_function  
GO:0003725   double-stranded RNA binding  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
11 198 1hru (A) 4 188 21.00 0 1 0.7 -0.78
27 150 1hru (A) 20 141 27.00 0.0000022 0.91 0.66 -0.95
1 205 1k7j (A) 1 203 16.00 0 1 0.635505 -0.53
2 359 3aje (A) 2 350 24.00 0 1 0.677985 0.5
4 289 3aje (A) 4 311 30.00 0 1 0.823788 -0.27
336 519 4uos (A) 0 184 18.00 0.032 0.15 0.578035 -1.06

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, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 16 hs, merozoite, early ring, late ring, Oocyst, Sporozoite, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 24 hs, gametocyte, early schizont, early trophozoite, late schizont, Male Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs. Otto TD
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_126848)

Species Accession Gene Product
Arabidopsis thaliana AT3G01920   Sua5/YciO/YrdC domain-containing protein
Babesia bovis BBOV_IV001880   translation factor Sua5, putative
Brugia malayi Bm1_41750   yrdC domain containing protein
Candida albicans CaO19.7088   Protein involved in translation initiation
Candida albicans CaO19_7088   hypothetical protein
Caenorhabditis elegans CELE_Y48C3A.18   Protein Y48C3A.18, isoform C
Cryptosporidium hominis Chro.10272   hypothetical protein
Cryptosporidium parvum cgd1_2420   SUA5 like RNA binding domain containing protein
Chlamydia trachomatis CT_137   SuA5 family protein
Dictyostelium discoideum DDB_G0278955   hypothetical protein
Drosophila melanogaster Dmel_CG33786   CG33786 gene product from transcript CG33786-RA
Escherichia coli b3282   tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein, threonine-dependent ADP-forming ATPase
Escherichia coli b1267   putative RNA binding protein
Echinococcus granulosus EgrG_000086900   yrdC domain containing protein
Entamoeba histolytica EHI_009260   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000086900   yrdc domain containing protein mitochondrial
Giardia lamblia GL50803_17389   SUA5 protein
Homo sapiens ENSG00000196449   yrdC N(6)-threonylcarbamoyltransferase domain containing
Leishmania braziliensis LbrM.28.2260   hypothetical protein, conserved
Leishmania donovani LdBPK_282210.1   tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family, putative
Leishmania infantum LinJ.28.2210   hypothetical protein, conserved
Leishmania major LmjF.28.2070   hypothetical protein, conserved
Leishmania mexicana LmxM.28.2070   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_04644   yrdC domain-containing protein
Mycobacterium leprae ML1136   conserved hypothetical protein
Mus musculus ENSMUSG00000028889   yrdC domain containing (E.coli)
Mycobacterium tuberculosis Rv1301   Conserved protein
Mycobacterium ulcerans MUL_3963   hypothetical protein
Neospora caninum NCLIV_000870   Sua5/YciO/YrdC/YwlC family protein, related
Oryza sativa 4346132   Os08g0531300
Oryza sativa 4331975   Os03g0201600
Onchocerca volvulus OVOC1560  
Plasmodium berghei PBANKA_0602500   threonylcarbamoyl-AMP synthase, putative
Plasmodium falciparum PF3D7_1203500   threonylcarbamoyl-AMP synthase, putative
Plasmodium knowlesi PKNH_1303300   threonylcarbamoyl-AMP synthase, putative
Plasmodium vivax PVX_084220   threonylcarbamoyl-AMP synthase, putative
Plasmodium yoelii PY05913   hypothetical protein
Saccharomyces cerevisiae YGL169W   Sua5p
Schistosoma japonicum Sjp_0073310   ko:K07566 putative translation factor, putative
Schistosoma mansoni Smp_127100   hypothetical protein
Schmidtea mediterranea mk4.042549.01  
Trypanosoma brucei gambiense Tbg972.11.9930   hypothetical protein, conserved
Trypanosoma brucei Tb927.11.8880   tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family, putative
Trypanosoma congolense TcIL3000.11.9190   tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family, putative
Trypanosoma cruzi TcCLB.508601.20   tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family, putative
Trypanosoma cruzi TcCLB.511801.50   tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family, putative
Toxoplasma gondii TGME49_294010   yrdC domain-containing protein
Treponema pallidum TP0182   hypothetical protein
Theileria parva TP03_0474   hypothetical protein, conserved
Trichomonas vaginalis TVAG_212040   sua5 protein, putative
Wolbachia endosymbiont of Brugia malayi Wbm0638   translation factor, SUA5

Essentiality

PF3D7_1203500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.0620 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.0620 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.0620 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.0620 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b1267 Escherichia coli non-essential goodall
b3282 Escherichia coli essential goodall
YGL169W Saccharomyces cerevisiae inviable yeastgenome
TGME49_294010 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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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User comments

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Gene identifier PF3D7_1203500 (Plasmodium falciparum), threonylcarbamoyl-AMP synthase, putative
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