Detailed view for PF3D7_0918800

Basic information

TDR Targets ID: 4863
Plasmodium falciparum, dihydrouridine synthase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.6369 | Length (AA): 577 | MW (Da): 67204 | Paralog Number: 0

Signal peptide: Y | GPI Anchor: N | Predicted trans-membrane segments: 2

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

PF01207   Dihydrouridine synthase (Dus)

Gene Ontology

Mouse over links to read term descriptions.
GO:0020011   apicoplast  
GO:0002943   GO:tRNA dihydrouridine synthesis  

GO:0050660   FAD binding  
GO:0017150   tRNA dihydrouridine synthase activity  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  
GO:0008033   tRNA processing  
GO:0055114   oxidation reduction  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 8 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
199 553 1vhn (A) 6 309 24.00 0 1 0.65 -0.83
200 363 1vhn (A) 7 162 31.00 0.0000000022 1 0.76 -1.23
196 551 3b0p (A) 2 318 34.00 0.0000000096 1 0.921584 -0.25
198 528 3b0p (A) 4 296 40.00 0 1 0.958757 -0.54
200 363 1vhn (A) 7 162 31.00 0.000000019 1 0.706329 -0.71
195 553 3b0p (A) 2 314 35.00 0.000000017 1 0.863564 -0.2
197 527 3b0p (A) 4 296 40.00 0 1 0.957353 -0.51
199 362 1vhn (A) 7 162 31.00 0.00000002 1 0.707422 -0.71

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, sporozoite, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, merozoite, early ring, early trophozoite, late ring, late trophozoite. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, late schizont, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile early schizont, Oocyst, Female Gametocyte, Male Gametocyte. PlasmoDB Zanghi G Lasonder E
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.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • 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

Orthologs

Ortholog group members (OG5_130830)

Species Accession Gene Product
Arabidopsis thaliana AT3G63510   FMN-linked oxidoreductases superfamily protein
Babesia bovis BBOV_I002610   dihydrouridine synthase (Dus) domain containing protein
Cryptosporidium hominis Chro.20381   uncharacterized protein family UPF0034
Cryptosporidium parvum cgd2_3570   YjbN-like Dus1p tRNA dihydouriding synthase Tim barrel
Dictyostelium discoideum DDB_G0277081   hypothetical protein
Escherichia coli b4049   tRNA-dihydrouridine synthase A
Neospora caninum NCLIV_039180   hypothetical protein
Oryza sativa 4335364   Os04g0278900
Plasmodium berghei PBANKA_0819700   dihydrouridine synthase, putative
Plasmodium falciparum PF3D7_0918800   dihydrouridine synthase, putative
Plasmodium knowlesi PKNH_0716800   dihydrouridine synthase, putative
Plasmodium vivax PVX_099355   tRNA-dihydrouridine synthase A, putative
Plasmodium yoelii PY06801   Uncharacterized protein family UPF0034, putative
Toxoplasma gondii TGME49_266880   dihydrouridine synthase, putative
Theileria parva TP01_0028   tRNA-dihydrouridine synthase A, putative

Essentiality

PF3D7_0918800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b4049 Escherichia coli non-essential goodall
PBANKA_0819700 Plasmodium berghei Slow plasmo
TGME49_266880 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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

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.

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_0918800 (Plasmodium falciparum), dihydrouridine synthase, putative
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