Detailed view for PF3D7_0209800

Basic information

TDR Targets ID: 3364
Plasmodium falciparum, ATP-dependent RNA helicase UAP56
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 5.8404 | Length (AA): 457 | MW (Da): 52224 | 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:0008150   biological_process  
GO:0005575   cellular_component  
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  

Metabolic Pathways

Purine metabolism (KEGG)
RNA transport (KEGG)
mRNA surveillance pathway (KEGG)
Spliceosome (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
1 457 2eyq (A) 508 961 14.00 0 1 0.89 0.25
56 457 1xti (A) 46 426 65.00 0 1 1.69 -1.27
293 449 1fuk (A) 233 389 38.00 0 1 0.99 -2.16
3 43 2epa (A) 30 72 5.00 0.15 0 0.124916 -0.59
18 454 4pxa (A) 143 576 22.00 0.000013 1 1.26944 -0.29
56 457 1xti (A) 46 426 65.00 0 1 1.64825 -0.77
307 410 3i32 (A) 223 335 34.00 0.00000000012 1 0.776171 -1.47

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, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Oocyst, Ring, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Sporozoite. Zanghi G
Show/Hide expression data references
  • 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
  • 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_127438)

Species Accession Gene Product
Arabidopsis thaliana AT5G11170   DEAD-box ATP-dependent RNA helicase 15
Arabidopsis thaliana AT5G11200   DEAD-box ATP-dependent RNA helicase 56
Babesia bovis BBOV_IV002750   eIF-4A-like DEAD family RNA helicase, putative
Brugia malayi Bm1_08205   Probable ATP-dependent RNA helicase p47 homolog, putative
Candida albicans CaO19.13092   similar to spliceosomal DExD helicase involved in mRNA nuclear export
Candida albicans CaO19.5647   similar to spliceosomal DExD helicase involved in mRNA nuclear export
Caenorhabditis elegans CELE_C26D10.2   Protein HEL-1, isoform A
Cryptosporidium hominis Chro.80448   helicase
Cryptosporidium parvum cgd8_3900   Sub2p like superfamily II helicase involved in snRNP biogenesis
Dictyostelium discoideum DDB_G0269932   ATP-dependent RNA helicase
Drosophila melanogaster Dmel_CG7269   Helicase at 25E
Echinococcus granulosus EgrG_000546900   spliceosome rna helicase bat1
Entamoeba histolytica EHI_151600   helicase, putative
Entamoeba histolytica EHI_036900   DEAD/DEAH box helicase, putative
Echinococcus multilocularis EmuJ_000546900   spliceosome rna helicase bat1
Giardia lamblia GL50803_16376   ATP-dependent RNA helicase p47, putative
Homo sapiens ENSG00000123136   DEAD (Asp-Glu-Ala-Asp) box polypeptide 39A
Homo sapiens ENSG00000198563   DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B
Leishmania braziliensis LbrM.21.1700   RNA helicase, putative
Leishmania donovani LdBPK_211820.1   ATP-dependent RNA helicase SUB2, putative
Leishmania infantum LinJ.21.1820   RNA helicase, putative
Leishmania major LmjF.21.1552   RNA helicase, putative
Leishmania mexicana LmxM.21.1552   RNA helicase, putative
Loa Loa (eye worm) LOAG_07751   ATP-dependent RNA helicase WM6
Loa Loa (eye worm) LOAG_13381   hypothetical protein
Mus musculus ENSMUSG00000005481   DEAD (Asp-Glu-Ala-Asp) box polypeptide 39
Mus musculus ENSMUSG00000019432   DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B
Neospora caninum NCLIV_059450   hypothetical protein
Oryza sativa 4326193   Os01g0550000
Oryza sativa 4326192   Os01g0549700
Onchocerca volvulus OVOC13444  
Plasmodium berghei PBANKA_0306800   ATP-dependent RNA helicase UAP56, putative
Plasmodium falciparum PF3D7_0209800   ATP-dependent RNA helicase UAP56
Plasmodium knowlesi PKNH_0411300   ATP-dependent RNA helicase UAP56, putative
Plasmodium vivax PVX_003945   ATP-dependent RNA helicase UAP56, putative
Plasmodium yoelii PY00326   DEAD/DEAH box helicase, putative
Saccharomyces cerevisiae YDL084W   ATP-dependent RNA helicase SUB2
Schistosoma japonicum Sjp_0000230   ko:K01509 adenosinetriphosphatase [EC3.6.1.3], putative
Schistosoma mansoni Smp_003660   DEAD box ATP-dependent RNA helicase
Schmidtea mediterranea mk4.018320.00  
Schmidtea mediterranea mk4.000388.00   Spliceosome RNA helicase DDX39B homolog
Trypanosoma brucei gambiense Tbg972.10.500   ATP-dependent DEAD/H RNA helicase, putative,DEAD box RNA helicase, putative
Trypanosoma brucei Tb927.10.540   ATP-dependent RNA helicase SUB2, putative
Trypanosoma congolense TcIL3000_10_400   ATP-dependent RNA helicase SUB2, putative
Trypanosoma cruzi TcCLB.508319.40   ATP-dependent RNA helicase SUB2, putative
Toxoplasma gondii TGME49_216860   DEAD (Asp-Glu-Ala-Asp) box polypeptide DDX39
Theileria parva TP03_0373   ATP-dependent RNA helicase, putative
Trichomonas vaginalis TVAG_179860   DEAD box ATP-dependent RNA helicase, putative

Essentiality

PF3D7_0209800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.540 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.540 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.540 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.540 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C26D10.2 Caenorhabditis elegans adult lethal wormbase
CELE_C26D10.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_C26D10.2 Caenorhabditis elegans larval arrest wormbase
CELE_C26D10.2 Caenorhabditis elegans larval lethal wormbase
CELE_C26D10.2 Caenorhabditis elegans slow growth wormbase
CELE_C26D10.2 Caenorhabditis elegans sterile wormbase
YDL084W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0306800 Plasmodium berghei Essential plasmo
TGME49_216860 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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.
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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

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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Gene identifier PF3D7_0209800 (Plasmodium falciparum), ATP-dependent RNA helicase UAP56
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