Detailed view for PF3D7_0405000

Basic information

TDR Targets ID: 3826
Plasmodium falciparum, ATP-dependent RNA helicase DDX51, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.2851 | Length (AA): 567 | MW (Da): 67689 | 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

PF00270   DEAD/DEAH box helicase
PF00271   Helicase conserved C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0004004   ATP-dependent RNA helicase activity  
GO:0008026   ATP-dependent helicase activity  
GO:0005524   ATP binding  
GO:0004386   helicase activity  
GO:0003676   nucleic acid binding  
GO:0016070   RNA metabolic process  

Metabolic Pathways

Purine metabolism (KEGG)

Structural information

Modbase 3D models:

There are 12 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
34 510 2eyq (A) 513 931 13.00 0 1 0.93 -0.11
106 498 1hv8 (A) 3 346 29.00 0 1 1.07 -1.34
109 345 1q0u (A) 4 211 16.00 0 0.69 0.55 -1.92
84 504 3ews (A) 66 454 24.00 0.00019 1 0.798504 0.54
121 567 3i5x (A) 117 558 22.00 0.00000000058 1 0.95536 0.03
139 208 3bor (A) 39 121 40.00 0.69 0.93 0.292457 1.04
351 494 2hjv (A) 213 344 25.00 0.014 1 0.617968 -1.14
386 498 2rb4 (A) 342 452 30.00 0.00085 0.99 0.497295 -0.59
117 563 3i5x (A) 117 558 22.00 0.00000000061 1 0.959661 0.03
135 204 3bor (A) 39 121 40.00 0.71 0.93 0.292034 1.04
347 490 2hjv (A) 213 344 25.00 0.015 1 0.618473 -1.14
382 494 2rb4 (A) 342 452 30.00 0.00089 0.99 0.49741 -0.59

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 - 24 hs, gametocyte, sporozoite, early ring, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, merozoite, early schizont, early trophozoite, late schizont, late trophozoite, Oocyst, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Sporozoite. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Male Gametocyte. 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.
  • 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.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_155664)

Species Accession Gene Product
Cryptosporidium hominis Chro.20019   hypothetical protein
Cryptosporidium parvum cgd2_110   Dbp6p, eIF4a-1 family RNA SFII helicase
Plasmodium berghei PBANKA_1002700   ATP-dependent RNA helicase DDX51, putative
Plasmodium falciparum PF3D7_0405000   ATP-dependent RNA helicase DDX51, putative
Plasmodium knowlesi PKNH_0303100   ATP-dependent RNA helicase DDX51, putative
Plasmodium vivax PVX_000990   ATP-dependent RNA helicase protein, putative
Plasmodium yoelii PY03896   ATP-dependent RNA helicase mss116, mitochondrial precursor

Essentiality

PF3D7_0405000 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1002700 Plasmodium berghei Essential plasmo
Show/Hide essentiality data references
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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

  • Assay for Adenosine 5'-Triphosphatase pH 7 (3.6.1.3 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

31 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier PF3D7_0405000 (Plasmodium falciparum), ATP-dependent RNA helicase DDX51, putative
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