Detailed view for PF3D7_0320800

Basic information

TDR Targets ID: 3705
Plasmodium falciparum, ATP-dependent RNA helicase DDX6
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.044 | Length (AA): 433 | MW (Da): 49413 | 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:0005524   ATP binding  
GO:0004386   helicase activity  
GO:0003676   nucleic acid binding  
GO:0008026   ATP-dependent helicase activity  

Metabolic Pathways

Purine metabolism (KEGG)
RNA degradation (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
1 428 2eyq (A) 511 944 20.00 0 1 1.06 0.05
58 262 1vec (A) 83 288 60.00 0 1 1.4 -2.41
60 432 1s2m (A) 46 418 72.00 0 1 1.9 -2.29
4 53 4is1 (C) 473 522 6.00 0.0000034 0 0.168573 -0.15
27 425 4d25 (A) 145 560 24.00 0.41 1 1.23618 -0.26
56 432 4ct4 (B) 92 469 69.00 0 1 1.79827 -1.45
60 432 1s2m (A) 46 418 72.00 0 1 1.81503 -1.41

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, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, sporozoite, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Oocyst, Sporozoite, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile merozoite. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, Ring. Otto TD Zanghi G
Show/Hide expression data references
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • 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.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.

Orthologs

Ortholog group members (OG5_127804)

Species Accession Gene Product
Arabidopsis thaliana AT2G45810   DEAD-box ATP-dependent RNA helicase 6
Arabidopsis thaliana AT3G61240   DEAD-box ATP-dependent RNA helicase 12
Arabidopsis thaliana AT4G00660   DEAD-box ATP-dependent RNA helicase 8
Babesia bovis BBOV_II006480   ATP-dependent RNA helicase, putative
Brugia malayi Bm1_30200   germline helicase protein 1
Candida albicans CaO19.6197   RNA helicase of DEAD box family
Candida albicans CaO19.13577   RNA helicase of DEAD box family
Caenorhabditis elegans CELE_C07H6.5   Protein CGH-1
Cryptosporidium hominis Chro.80211   ATP-dependent RNA helicase
Cryptosporidium parvum cgd8_1820   ATP-dependent RNA helicase, putative
Dictyostelium discoideum DDB_G0291804   DEAD/DEAH box helicase
Drosophila melanogaster Dmel_CG4916   maternal expression at 31B
Echinococcus granulosus EgrG_001180000   ATP dependent RNA helicase me31b
Echinococcus granulosus EgrG_000123700   ATP dependent RNA helicase DDX6
Echinococcus granulosus EgrG_001179800   e3 ubiquitin protein ligase RFWD3
Echinococcus multilocularis EmuJ_000123700   ATP dependent RNA helicase DDX6
Echinococcus multilocularis EmuJ_001180000   ATP dependent RNA helicase me31b
Echinococcus multilocularis EmuJ_001179800   e3 ubiquitin protein ligase RFWD3
Giardia lamblia GL50803_2098   ATP-dependent RNA helicase p54, putative
Homo sapiens ENSG00000110367   DEAD (Asp-Glu-Ala-Asp) box helicase 6
Leishmania donovani LdBPK_350370.1   ATP-dependent DEAD-box RNA helicase, putative
Leishmania infantum LinJ.35.0370   ATP-dependent DEAD-box RNA helicase, putative
Leishmania major LmjF.35.0370   ATP-dependent DEAD-box RNA helicase, putative
Leishmania mexicana LmxM.34.0370   ATP-dependent DEAD-box RNA helicase, putative
Loa Loa (eye worm) LOAG_02698   ATP-dependent RNA helicase DHH1
Mus musculus ENSMUSG00000032097   DEAD (Asp-Glu-Ala-Asp) box polypeptide 6
Neospora caninum NCLIV_056360   Eukaryotic initiation factor, related
Oryza sativa 4349053   Os10g0503700
Oryza sativa 4336501   Os04g0533000
Oryza sativa 4330120   Os02g0641800
Plasmodium berghei PBANKA_1217700   ATP-dependent RNA helicase DDX6
Plasmodium falciparum PF3D7_0320800   ATP-dependent RNA helicase DDX6
Plasmodium knowlesi PKNH_0820000   ATP-dependent RNA helicase DDX6, putative
Plasmodium vivax PVX_095195   ATP-dependent RNA helicase DDX6, putative
Plasmodium yoelii PY01870   ATP-dependent RNA Helicase
Saccharomyces cerevisiae YDL160C   DExD/H-box ATP-dependent RNA helicase DHH1
Schistosoma japonicum Sjp_0311860   RING finger and WD repeat domain-containing protein 3, putative
Schistosoma japonicum Sjp_0043670   ko:K08849 mixed lineage kinase domain-like, putative
Schistosoma japonicum Sjp_0036950   ko:K01509 adenosinetriphosphatase [EC3.6.1.3], putative
Schistosoma mansoni Smp_173970   DEAD box ATP-dependent RNA helicase
Schmidtea mediterranea mk4.018587.01   Probable ATP-dependent RNA helicase DDX6
Schmidtea mediterranea mk4.005911.00   Probable ATP-dependent RNA helicase DDX6
Schmidtea mediterranea mk4.000222.07   Probable ATP-dependent RNA helicase DDX6
Schmidtea mediterranea mk4.002614.04   Probable ATP-dependent RNA helicase DDX6
Schmidtea mediterranea mk4.007746.03   ATP-dependent RNA helicase cgh-1
Schmidtea mediterranea mk4.021485.01   Probable ATP-dependent RNA helicase DDX6
Schmidtea mediterranea mk4.020079.00   Probable ATP-dependent RNA helicase DDX6
Trypanosoma brucei gambiense Tbg972.10.4980   hypothetical protein, conserved,ATP-dependent DEAD-box RNA helicase, putative
Trypanosoma brucei Tb927.10.3990   DHH1
Trypanosoma congolense TcIL3000_10_3320   ATP-dependent DEAD-box RNA helicase, putative
Trypanosoma cruzi TcCLB.506959.30   ATP-dependent DEAD/H RNA helicase, putative
Toxoplasma gondii TGME49_313010   DEAD (Asp-Glu-Ala-Asp) box polypeptide DDX6
Theileria parva TP02_0613   ATP-dependent RNA helicase, putative

Essentiality

PF3D7_0320800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.3990 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.3990 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.3990 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.3990 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C07H6.5 Caenorhabditis elegans adult lethal wormbase
CELE_C07H6.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_C07H6.5 Caenorhabditis elegans larval arrest wormbase
CELE_C07H6.5 Caenorhabditis elegans larval lethal wormbase
CELE_C07H6.5 Caenorhabditis elegans sterile wormbase
PBANKA_1217700 Plasmodium berghei Dispensable plasmo
TGME49_313010 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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
  • 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.
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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

Druggability index (range: 0 to 1): 0.2

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.

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Gene identifier PF3D7_0320800 (Plasmodium falciparum), ATP-dependent RNA helicase DDX6
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