Detailed view for PF3D7_0504400

Basic information

TDR Targets ID: 4074
Plasmodium falciparum, ATP-dependent helicase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.6447 | Length (AA): 755 | MW (Da): 87598 | 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
PF08152   GUCT (NUC152) domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0020011   apicoplast  
GO:0005634   nucleus  
GO:0008026   ATP-dependent helicase activity  
GO:0005524   ATP binding  
GO:0004386   helicase activity  
GO:0003723   RNA binding  
GO:0003676   nucleic acid binding  

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
4 753 2eyq (A) 449 1116 13.00 0 1 0.67 0.81
404 563 1fuk (A) 233 388 28.00 0 1 0.67 -1.64
161 717 4f92 (B) 476 1021 21.00 0.69 1 0.638548 0.83
167 388 3ber (A) 48 223 41.00 0 1 0.58584 -0.58
144 710 1oyw (A) 4 514 14.00 0.0000000000055 1 0.774693 0.86
167 388 3ber (A) 48 223 41.00 0 1 0.59674 -0.69
167 387 1wrb (A) 208 394 38.00 0 1 0.561415 -0.45
255 388 2oxc (A) 128 261 33.00 0.000000071 1 0.749183 -1.78

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 - 32 hs, early schizont, early trophozoite, late trophozoite. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, late ring, late schizont, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, merozoite, sporozoite, early ring, Female Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, Ring, Sporozoite, Male Gametocyte. Otto TD Zanghi G Lasonder E
Show/Hide expression data references
  • 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.
  • 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

Orthologs

Ortholog group members (OG5_128505)

Species Accession Gene Product
Arabidopsis thaliana AT3G22310   DEAD-box ATP-dependent RNA helicase
Arabidopsis thaliana AT5G62190   DEAD/DEAH box RNA helicase PRH75
Arabidopsis thaliana AT3G22330   putative mitochondrial RNA helicase 2
Arabidopsis thaliana AT5G26742   DEAD-box ATP-dependent RNA helicase 3
Cryptosporidium hominis Chro.60561   DEAD/DEAH box helicase
Cryptosporidium parvum cgd6_4860   nucleolar protein GU2. eIF4A-1-family. RNA SFII helicase
Echinococcus granulosus EgrG_000068900   DEAD Asp Glu Ala Asp box polypeptide 21
Entamoeba histolytica EHI_119920   DEAD/DEAH box helicase, putative
Echinococcus multilocularis EmuJ_000068900   DEAD (Asp Glu Ala Asp) box polypeptide 21
Homo sapiens ENSG00000107625   DEAD (Asp-Glu-Ala-Asp) box polypeptide 50
Homo sapiens ENSG00000165732   DEAD (Asp-Glu-Ala-Asp) box helicase 21
Leishmania braziliensis LbrM.05.0140   nucleolar RNA helicase II, putative
Leishmania donovani LdBPK_050140.1   nucleolar RNA helicase II, putative
Leishmania infantum LinJ.05.0140   nucleolar RNA helicase II, putative
Leishmania major LmjF.05.0140   nucleolar RNA helicase II, putative
Leishmania mexicana LmxM.05.0140   nucleolar RNA helicase II, putative
Mus musculus ENSMUSG00000020075   DEAD (Asp-Glu-Ala-Asp) box polypeptide 21
Mus musculus ENSMUSG00000020076   DEAD (Asp-Glu-Ala-Asp) box polypeptide 50
Mycobacterium tuberculosis Rv3211   Probable ATP-dependent RNA helicase RhlE
Mycobacterium ulcerans MUL_2533   ATP-dependent RNA helicase RhlE
Neospora caninum NCLIV_005540   hypothetical protein
Neospora caninum NCLIV_053820   DEAD box RNA helicase, related
Oryza sativa 4347610   Os09g0520700
Oryza sativa 4334649   Os03g0827700
Plasmodium berghei PBANKA_1104000   ATP-dependent helicase, putative
Plasmodium falciparum PF3D7_0504400   ATP-dependent helicase, putative
Plasmodium knowlesi PKNH_1029200   ATP-dependent helicase, putative
Plasmodium vivax PVX_097785   ATP-dependent helicase, putative
Plasmodium yoelii PY03841   Unknown protein
Schistosoma mansoni Smp_157800   DEAD box ATP-dependent RNA helicase
Schmidtea mediterranea mk4.013834.00   Putative dead box ATP-dependent RNA helicase
Trypanosoma brucei gambiense Tbg972.5.5960   nucleolar RNA helicase II, putative,nucleolar RNA helicase Gu, putative
Trypanosoma brucei Tb927.5.4420   nucleolar RNA helicase II, putative
Trypanosoma brucei Tb05.5K5.70   nucleolar RNA helicase II, putative
Trypanosoma congolense TcIL3000_0_18690   nucleolar RNA helicase II, putative
Trypanosoma congolense TcIL3000_5_5060   nucleolar RNA helicase II, putative
Trypanosoma cruzi TcCLB.508205.20   nucleolar RNA helicase II, putative
Trypanosoma cruzi TcCLB.506123.40   nucleolar RNA helicase II, putative
Toxoplasma gondii TGME49_222140   DEAD/DEAH box helicase domain-containing protein
Toxoplasma gondii TGME49_309570   DEAD/DEAH box helicase domain-containing protein

Essentiality

PF3D7_0504400 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.5.4420 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.5.4420 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.5.4420 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.5.4420 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_1104000 Plasmodium berghei Essential plasmo
TGME49_222140 Toxoplasma gondii Probably essential sidik
TGME49_309570 Toxoplasma gondii Probably essential sidik
TGME49_222140 Toxoplasma gondii Essentiality uncertain sidik
TGME49_309570 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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.
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.

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.

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Gene identifier PF3D7_0504400 (Plasmodium falciparum), ATP-dependent helicase, putative
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