Detailed view for PF3D7_0521700

Basic information

TDR Targets ID: 4248
Plasmodium falciparum, ATP-dependent RNA helicase DDX1, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.921 | Length (AA): 841 | MW (Da): 97338 | Paralog Number: 0

Signal peptide: N | 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

PF00270   DEAD/DEAH box helicase
PF00271   Helicase conserved C-terminal domain
PF00622   SPRY domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0008026   ATP-dependent helicase activity  
GO:0005524   ATP binding  
GO:0005515   protein binding  
GO:0004386   helicase activity  
GO:0003676   nucleic acid binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 7 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
250 715 2db3 (A) 225 599 22.00 0 1 0.59 0.14
295 485 1q0u (A) 24 211 22.00 0.000000078 1 0.65 -1.48
3 57 3iuy (A) 235 286 46.00 0.024 0.48 0.478798 0.36
4 66 3ber (A) 26 88 43.00 0.00063 0.99 0.690311 -0.95
339 717 1hv8 (A) 70 348 31.00 0 1 0.439054 0.53
575 706 2hjv (A) 226 341 37.00 0.0000000022 1 0.630356 -1.42
609 729 1hv8 (A) 242 362 27.00 0.34 1 0.559476 -0.77

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 60-80% percentile merozoite, sporozoite, early ring, early trophozoite, late ring, Ring. PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, early schizont, late trophozoite, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, Oocyst, Female Gametocyte, Male Gametocyte. Otto TD 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_130919)

Species Accession Gene Product
Babesia bovis BBOV_III003880   DEAD/DEAH box helicase domain containing protein
Brugia malayi Bm1_11355   ATP-dependent helicase DDX1
Caenorhabditis elegans CELE_Y55F3BR.1   Protein Y55F3BR.1
Dictyostelium discoideum DDB_G0269966   DEAD/DEAH box helicase
Drosophila melanogaster Dmel_CG9054   Dead-box-1
Echinococcus granulosus EgrG_000545600   ATP dependent RNA helicase Ddx1
Echinococcus multilocularis EmuJ_000545600   ATP dependent RNA helicase Ddx1
Homo sapiens ENSG00000079785   DEAD (Asp-Glu-Ala-Asp) box helicase 1
Loa Loa (eye worm) LOAG_08173   ATP-dependent helicase DDX1
Loa Loa (eye worm) LOAG_05806   hypothetical protein
Mus musculus ENSMUSG00000037149   DEAD (Asp-Glu-Ala-Asp) box polypeptide 1
Neospora caninum NCLIV_002510   ATP-dependent RNA helicase DDX family protein, putative
Plasmodium berghei PBANKA_1236300   ATP-dependent RNA helicase DDX1, putative
Plasmodium falciparum PF3D7_0521700   ATP-dependent RNA helicase DDX1, putative
Plasmodium knowlesi PKNH_1011200   ATP-dependent RNA helicase DDX1, putative
Plasmodium vivax PVX_080160   DEAD/DEAH box ATP-dependent RNA helicase, putative
Plasmodium yoelii PY01366   ATP-dependent helicase ddx1
Schistosoma japonicum Sjp_0011260   ATP-dependent RNA helicase DDX1, putative
Schistosoma japonicum Sjp_0003220   ko:K01509 adenosinetriphosphatase [EC3.6.1.3], putative
Schistosoma japonicum Sjp_0008650   ATP-dependent RNA helicase DDX1, putative
Schistosoma japonicum Sjp_0217350   ATP-dependent RNA helicase DDX1, putative
Schistosoma mansoni Smp_163110   DEAD box ATP-dependent RNA helicase
Schmidtea mediterranea mk4.008454.02  
Schmidtea mediterranea mk4.004138.02  
Schmidtea mediterranea mk4.004138.01   ATP-dependent RNA helicase DDX1
Schmidtea mediterranea mk4.004138.03  
Toxoplasma gondii TGME49_207430   ATP-dependent RNA helicase DDX1, putative

Essentiality

PF3D7_0521700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_Y55F3BR.1 Caenorhabditis elegans slow growth wormbase
TGME49_207430 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • 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.
  • 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.
  • 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

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_0521700 (Plasmodium falciparum), ATP-dependent RNA helicase DDX1, putative
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