Detailed view for PF3D7_1134700

Basic information

TDR Targets ID: 1827
Plasmodium falciparum, DNA-directed RNA polymerase I subunit RPA2, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.1953 | Length (AA): 1517 | MW (Da): 175532 | 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

PF00562   RNA polymerase Rpb2, domain 6
PF04560   RNA polymerase Rpb2, domain 7
PF04563   RNA polymerase beta subunit
PF04565   RNA polymerase Rpb2, domain 3

Gene Ontology

Mouse over links to read term descriptions.
GO:0005736   DNA-directed RNA polymerase I complex  
GO:0032549   ribonucleoside binding  
GO:0006360   transcription from RNA polymerase I promoter  
GO:0006351   transcription, DNA-dependent  
GO:0003899   DNA-directed RNA polymerase activity  
GO:0003677   DNA binding  
GO:0006350   transcription  

Metabolic Pathways

Purine metabolism (KEGG)
Pyrimidine metabolism (KEGG)
Global map (KEGG)
RNA polymerase (KEGG)

Structural information

Modbase 3D models:

There are 5 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
1012 1435 1ynj (C) 669 1061 31.00 0 1 0.24 1.35
3 205 4tql (A) 17 224 9.00 0.1 0.02 0.196317 -0.27
45 1513 1k83 (B) 19 1224 28.00 0 1 0.767159 1.71
287 529 3fhn (A) 307 535 25.00 0.22 0.81 0.253885 0.43
1146 1432 5byh (C) 1048 1296 35.00 0 0.17 0.213889 1.68

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, sporozoite, early ring, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile merozoite, early trophozoite, late ring. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, late trophozoite, Oocyst, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Sporozoite, Female Gametocyte. Zanghi G Lasonder E
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.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • 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_127929)

Species Accession Gene Product
Arabidopsis thaliana AT1G29940   nuclear RNA polymerase A2
Babesia bovis BBOV_II001980   DNA-directed RNA polymerase, beta subunit, putative
Brugia malayi Bm1_28405   DNA-directed RNA polymerase, beta subunit family protein
Candida albicans CaO19.7062   DNA-directed RNA polymerase I
Candida albicans CaO19_7062   hypothetical protein
Caenorhabditis elegans CELE_F14B4.3   Protein RPOA-2
Cryptosporidium hominis Chro.10312   DNA-directed RNA polymerase I polypeptide 2 (RNA polymerase I subunit 2)
Cryptosporidium parvum cgd1_2770   RNA polymerase 1 beta subunit
Dictyostelium discoideum DDB_G0293560   RNA polymerase I, second largest subunit
Drosophila melanogaster Dmel_CG4033   RNA polymerase I 135kD subunit
Echinococcus granulosus EgrG_000877300   DNA directed RNA polymerase I subunit RPA2
Entamoeba histolytica EHI_186020   DNA-directed RNA polymerase subunit, putative
Echinococcus multilocularis EmuJ_000877300   DNA directed RNA polymerase I subunit RPA2
Giardia lamblia GL50803_29436   DNA-directed RNA polymerase subunit B
Homo sapiens ENSG00000125630   polymerase (RNA) I polypeptide B, 128kDa
Leishmania braziliensis LbrM.25.2130   RNA polymerase I second largest subunit, putative
Leishmania donovani LdBPK_250630.1   RNA polymerase I second largest subunit, putative
Leishmania infantum LinJ.25.0630   RNA polymerase I second largest subunit, putative
Leishmania major LmjF.25.0620   RNA polymerase I second largest subunit, putative
Leishmania mexicana LmxM.25.0620   RNA polymerase I second largest subunit, putative
Loa Loa (eye worm) LOAG_04227   DNA-directed RNA polymerase
Loa Loa (eye worm) LOAG_04226   hypothetical protein
Mus musculus ENSMUSG00000027395   polymerase (RNA) I polypeptide B
Neospora caninum NCLIV_006540   DNA-directed RNA polymerase (EC 2.7.7.6), related
Plasmodium berghei PBANKA_0913800   DNA-directed RNA polymerase I subunit RPA2, putative
Plasmodium falciparum PF3D7_1134700   DNA-directed RNA polymerase I subunit RPA2, putative
Plasmodium knowlesi PKNH_0932900   DNA-directed RNA polymerase I subunit RPA2, putative
Plasmodium vivax PVX_092345   DNA-directed RNA polymerase I subunit RPA2, putative
Plasmodium yoelii PY05002   DNA-directed RNA polymerase, beta subunit
Saccharomyces cerevisiae YPR010C   DNA-directed RNA polymerase I core subunit RPA135
Schistosoma japonicum Sjp_0038750   ko:K03002 DNA-directed RNA polymerase I subunit A2, putative
Schistosoma mansoni Smp_140690   DNA-directed RNA polymerase I subunit
Schmidtea mediterranea mk4.001820.02   DNA-directed RNA polymerase I subunit RPA2
Schmidtea mediterranea mk4.001820.03   DNA-directed RNA polymerase I subunit RPA2
Trypanosoma brucei gambiense Tbg972.11.610   RNA polymerase I second largest subunit, putative
Trypanosoma brucei Tb927.11.630   RNA polymerase I second largest subunit
Trypanosoma cruzi TcCLB.506925.40   RNA polymerase I second largest subunit, putative
Toxoplasma gondii TGME49_297530   DNA-directed RNA polymerase I RPA2
Theileria parva TP04_0334   DNA-directed RNA polymerase, beta subunit, putative
Trichomonas vaginalis TVAG_353520   DNA-directed RNA polymerase I subunit, putative

Essentiality

PF3D7_1134700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.03.0450 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.03.0450 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.03.0450 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.03.0450 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F14B4.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_F14B4.3 Caenorhabditis elegans larval arrest wormbase
CELE_F14B4.3 Caenorhabditis elegans larval lethal wormbase
CELE_F14B4.3 Caenorhabditis elegans slow growth wormbase
YPR010C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0913800 Plasmodium berghei Essential plasmo
TGME49_297530 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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.

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): 0.5

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 Ribonucleic Acid Polymerase (2.7.7.6 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

16 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.

User comments

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Gene identifier PF3D7_1134700 (Plasmodium falciparum), DNA-directed RNA polymerase I subunit RPA2, putative
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