Detailed view for PF3D7_1021500

Basic information

TDR Targets ID: 1283
Plasmodium falciparum, ATP-dependent RNA helicase ROK1, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.0042 | Length (AA): 680 | MW (Da): 79862 | 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:0005575   cellular_component  
GO:0003724   RNA helicase activity  
GO:0008150   biological_process  
GO:0008026   ATP-dependent helicase activity  
GO:0005524   ATP 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 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
39 680 2eyq (A) 455 1001 12.00 0 1 0.66 0.45
451 610 2g2j (A) 308 471 28.00 0 1 0.59 -2.02
1 174 4tql (A) 38 217 10.00 0.43 0.03 0.398382 -0.93
146 615 4nho (A) 354 797 26.00 0 1 0.793576 0.01
192 628 4w7s (A) 184 580 28.00 0 1 0.797047 -0.01
454 572 2p6n (A) 407 522 37.00 0.00000035 1 0.6614 -0.63
478 611 2hjv (A) 236 368 30.00 0.0014 1 0.691059 -1.18
545 614 2p6n (A) 495 564 31.00 0.39 0.84 0.440941 -0.38

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, gametocyte, sporozoite, early ring, late ring. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, merozoite, early schizont, early trophozoite, late trophozoite, Ring, Sporozoite, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs, late schizont, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 40 hs, Male Gametocyte. Otto TD Lasonder E
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • 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.

Orthologs

Ortholog group members (OG5_128422)

Species Accession Gene Product
Arabidopsis thaliana AT3G09720   DEAD-box ATP-dependent RNA helicase 57
Babesia bovis BBOV_IV006910   DEAD box RNA helicase, putative
Candida albicans CaO19.11240   DEAD box RNA helicase similar to S. cerevisiae ROK1 (YGL171W) required for 18S rRNA synthesis
Candida albicans CaO19.3756   DEAD box RNA helicase similar to S. cerevisiae ROK1 (YGL171W) required for 18S rRNA synthesis
Caenorhabditis elegans CELE_R05D11.4   Protein R05D11.4
Cryptosporidium hominis Chro.60373   dead box RNA helicase
Cryptosporidium parvum cgd6_3210   Rok1p, eIF4A-1-family RNA SFII helicase
Dictyostelium discoideum DDB_G0274325   DEAD/DEAH box helicase
Drosophila melanogaster Dmel_CG5589   CG5589 gene product from transcript CG5589-RA
Echinococcus granulosus EgrG_000511750   ATP dependent RNA helicase DDX52
Echinococcus multilocularis EmuJ_000511750   ATP dependent RNA helicase DDX52
Giardia lamblia GL50803_14451   ATP-dependent RNA helicase
Homo sapiens 11056   DEAD (Asp-Glu-Ala-Asp) box polypeptide 52
Leishmania braziliensis LbrM.32.0650   ATP-dependent RNA helicase-like protein, putative,RNA helicase, putative
Leishmania donovani LdBPK_320600.1   ATP- dependent RNA helicase, putative
Leishmania infantum LinJ.32.0600   ATP-dependent RNA helicase-like protein, putative,RNA helicase, putative
Leishmania major LmjF.32.0570   ATP-dependent RNA helicase-like protein, putative,RNA helicase, putative
Leishmania mexicana LmxM.31.0570   ATP-dependent RNA helicase-like protein, putative,RNA helicase, putative
Mus musculus ENSMUSG00000020677   DEAD (Asp-Glu-Ala-Asp) box polypeptide 52
Neospora caninum NCLIV_007630   ATP-dependent RNA helicase, putative
Oryza sativa 4344113   Os07g0647900
Plasmodium berghei PBANKA_0505700   ATP-dependent RNA helicase ROK1, putative
Plasmodium falciparum PF3D7_1021500   ATP-dependent RNA helicase ROK1, putative
Plasmodium knowlesi PKNH_0605800   ATP-dependent RNA helicase ROK1, putative
Plasmodium vivax PVX_001940   ATP-dependent RNA helicase, putative
Plasmodium yoelii PY02253   putative ATP-dependent RNA helicase c22f3.08c
Saccharomyces cerevisiae YGL171W   RNA-dependent ATPase ROK1
Schistosoma japonicum Sjp_0214930   ko:K01529 similar to ATP-dependent RNA helicase ROK1 isoform a [EC:3.6.1.-], putative
Schistosoma mansoni Smp_047110   DEAD box ATP-dependent RNA helicase
Schmidtea mediterranea mk4.000199.04   Putative dead box ATP-dependent RNA helicase
Trypanosoma brucei gambiense Tbg972.11.15430   ATP-dependent DEAD/H RNA helicase, putative,ATP- dependent RNA helicase, putative
Trypanosoma brucei Tb927.11.13810   ATP- dependent RNA helicase, putative
Trypanosoma congolense TcIL3000.11.14180   ATP- dependent RNA helicase, putative
Trypanosoma cruzi TcCLB.509161.130   ATP- dependent RNA helicase, putative
Toxoplasma gondii TGME49_253090   DEAD/DEAH box helicase domain-containing protein
Theileria parva TP03_0216   RNA helicase, putative
Trichomonas vaginalis TVAG_335860   DEAD box ATP-dependent RNA helicase, putative

Essentiality

PF3D7_1021500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.5370 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.5370 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.5370 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.5370 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
YGL171W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0505700 Plasmodium berghei Slow plasmo
TGME49_253090 Toxoplasma gondii Probably essential 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
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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
  • 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

Druggability index (range: 0 to 1): 0.3

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.

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier PF3D7_1021500 (Plasmodium falciparum), ATP-dependent RNA helicase ROK1, putative
Title for this comment
Comment