Detailed view for PF3D7_0215700

Basic information

TDR Targets ID: 3420
Plasmodium falciparum, DNA-directed RNA polymerase II subunit RPB2, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.5086 | Length (AA): 1340 | MW (Da): 151723 | Paralog Number: 1

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG3

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
PF04561   RNA polymerase Rpb2, domain 2
PF04563   RNA polymerase beta subunit
PF04565   RNA polymerase Rpb2, domain 3
PF04566   RNA polymerase Rpb2, domain 4
PF04567   RNA polymerase Rpb2, domain 5

Gene Ontology

Mouse over links to read term descriptions.
GO:0032549   ribonucleoside binding  
GO:0006351   transcription, DNA-dependent  
GO:0005665   DNA-directed RNA polymerase II, core complex  
GO:0003899   DNA-directed RNA polymerase activity  
GO:0003677   DNA binding  
GO:0006366   transcription from RNA polymerase II promoter  
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
40 1345 2a6h (C) 9 1111 22.00 0 1 0.6 1.48
24 1338 1k83 (B) 18 1219 56.00 0 1 1.28444 0.97
26 341 5c4x (B) 20 336 40.00 0 1 0.538921 1.44
29 1339 3h0g (B) 10 1208 56.00 0 1 1.29046 1.38
946 1084 4uos (A) 6 144 6.00 0.46 0 0.194831 -0.51

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 - 16 hs, intra-erythrocytic - 24 hs, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late trophozoite, Ring, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, gametocyte, late schizont, Oocyst, Sporozoite, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 48 hs. Otto TD
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.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_126694)

Species Accession Gene Product
Arabidopsis thaliana AT5G45140   DNA-directed RNA polymerase RPC2
Arabidopsis thaliana AT3G18090   DNA-directed RNA polymerase D subunit 2b
Arabidopsis thaliana AT4G21710   DNA-directed RNA polymerase II subunit RPB2
Arabidopsis thaliana AT3G23780   nuclear RNA polymerase D2A
Babesia bovis BBOV_III000960   DNA-directed RNA polymerase, beta subunit, putative
Babesia bovis BBOV_II002050   DNA-directed RNA polymerase, beta subunit family protein
Brugia malayi Bm1_16400   DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide
Brugia malayi Bm1_45495   DNA-directed RNA polymerase II second largest subunit, putative
Candida albicans CaO19.13269   Coatomer alpha chain of secretory pathway vesicles
Candida albicans CaO19.5847   Coatomer alpha chain of secretory pathway vesicles
Candida albicans CaO19.10857   DNA-dependent RNA polymerase II
Candida albicans CaO19.3349   DNA-dependent RNA polymerase II
Caenorhabditis elegans CELE_C26E6.4   Protein RPB-2
Caenorhabditis elegans CELE_F09F7.3   Protein RPC-2
Cryptosporidium hominis Chro.70415   DNA-directed RNA polymerase (EC 2.7.7.6) II second largest chain
Cryptosporidium hominis Chro.80027   DNA-directed RNA polymerase, beta subunit
Cryptosporidium parvum cgd8_170   DNA-directed RNA polymerase beta subunit
Cryptosporidium parvum cgd7_3720   RNA polymerase beta subunit
Dictyostelium discoideum DDB_G0288257   RNA polymerase II core subunit
Dictyostelium discoideum DDB_G0288449   RNA polymerase III, second largest subunit
Drosophila melanogaster Dmel_CG3180   RNA polymerase II 140kD subunit
Drosophila melanogaster Dmel_CG8344   RNA polymerase III 128kD subunit
Echinococcus granulosus EgrG_000604200   DNA directed RNA polymerase II subunit RPB2
Echinococcus granulosus EgrG_000607400   DNA directed RNA polymerase III subunit RPC2
Entamoeba histolytica EHI_022940   DNA-directed RNA polymerase subunit, putative
Entamoeba histolytica EHI_095860   DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide, putative
Echinococcus multilocularis EmuJ_000604200   DNA directed RNA polymerase II subunit RPB2
Echinococcus multilocularis EmuJ_000607400   DNA directed RNA polymerase III subunit RPC2
Giardia lamblia GL50803_17448   DNA-directed RNA polymerase RPB2
Giardia lamblia GL50803_17187   DNA-directed RNA polymerase subunit B
Homo sapiens ENSG00000013503   polymerase (RNA) III (DNA directed) polypeptide B
Homo sapiens ENSG00000047315   polymerase (RNA) II (DNA directed) polypeptide B, 140kDa
Leishmania braziliensis LbrM.31.0270   DNA-directed RNA polymerase II subunit 2, putative
Leishmania braziliensis LbrM.20.4090   DNA-directed RNA polymerase polypeptide
Leishmania donovani LdBPK_310170.1   DNA-directed RNA polymerase II subunit 2, putative
Leishmania infantum LinJ.31.0170   DNA-directed RNA polymerase II subunit 2, putative
Leishmania infantum LinJ.20.0010   DNA-directed RNA polymerase polypeptide, putative
Leishmania major LmjF.20.0010   DNA-directed RNA polymerase polypeptide, putative
Leishmania mexicana LmxM.30.0160   DNA-directed RNA polymerase II subunit 2, putative
Leishmania mexicana LmxM.20.0010   DNA-directed RNA polymerase polypeptide, putative
Loa Loa (eye worm) LOAG_06607   DNA-directed RNA polymerase II second largest subunit
Loa Loa (eye worm) LOAG_10764   hypothetical protein
Loa Loa (eye worm) LOAG_09641   RNA polymerase III 128kD subunit-PA
Mus musculus ENSMUSG00000034453   polymerase (RNA) III (DNA directed) polypeptide B
Mus musculus ENSMUSG00000029250   polymerase (RNA) II (DNA directed) polypeptide B
Neospora caninum NCLIV_028180   DNA-directed RNA polymerase subunit beta
Neospora caninum NCLIV_034580   DNA-directed RNA polymerase (EC 2.7.7.6), related
Oryza sativa 4344774   Os08g0171600
Oryza sativa 4337169   Os04g0641000
Oryza sativa 4333571   Os03g0646800
Oryza sativa 4333066   Os03g0403100
Plasmodium berghei PBANKA_0605200   DNA-directed RNA polymerase III subunit RPC2, putative
Plasmodium berghei PBANKA_0312400   DNA-directed RNA polymerase II subunit RPB2, putative
Plasmodium falciparum PF3D7_0215700   DNA-directed RNA polymerase II subunit RPB2, putative
Plasmodium falciparum PF3D7_1206600   DNA-directed RNA polymerase III subunit RPC2, putative
Plasmodium knowlesi PKNH_0405200   DNA-directed RNA polymerase II subunit RPB2, putative
Plasmodium knowlesi PKNH_1306600   DNA-directed RNA polymerase III subunit RPC2, putative
Plasmodium vivax PVX_084365   DNA-directed RNA polymerase III subunit, putative
Plasmodium vivax PVX_002755   DNA-directed RNA polymerase II subunit RPB2, putative
Plasmodium yoelii PY01847   DNA-directed RNA polymerase, beta subunit, putative
Plasmodium yoelii PY01115   DNA-directed RNA polymerase, beta subunit
Saccharomyces cerevisiae YOR207C   DNA-directed RNA polymerase III core subunit RET1
Saccharomyces cerevisiae YOR151C   DNA-directed RNA polymerase II core subunit RPB2
Schistosoma japonicum Sjp_0118110   DNA-directed RNA polymerase III subunit RPC2, putative
Schistosoma japonicum Sjp_0300010   ko:K03010 DNA-directed RNA polymerase II subunit B, putative
Schistosoma japonicum Sjp_0204820   DNA-directed RNA polymerase III subunit RPC2, putative
Schistosoma japonicum Sjp_0109500   DNA-directed RNA polymerase III subunit RPC2, putative
Schistosoma japonicum Sjp_0099180   DNA-directed RNA polymerase III subunit RPC2, putative
Schistosoma japonicum Sjp_0111260   DNA-directed RNA polymerase III subunit RPC2, putative
Schistosoma mansoni Smp_153760.2   DNA-directed RNA polymerase III subunit
Schistosoma mansoni Smp_130680   DNA-directed rna polymerase II subunit
Schistosoma mansoni Smp_153760.1   DNA-directed RNA polymerase III subunit
Schmidtea mediterranea mk4.044745.00   DNA-directed RNA polymerase II subunit RPB2
Schmidtea mediterranea mk4.000049.18   DNA-directed RNA polymerase III subunit RPC2
Schmidtea mediterranea mk4.015160.07  
Schmidtea mediterranea mk4.007730.05   DNA-directed RNA polymerase II subunit RPB2
Schmidtea mediterranea mk4.009506.01  
Schmidtea mediterranea mk4.006422.02  
Schmidtea mediterranea mk4.010348.00   DNA-directed RNA polymerase II subunit RPB2
Schmidtea mediterranea mk4.071695.00   DNA-directed RNA polymerase II subunit RPB2
Schmidtea mediterranea mk4.010348.01  
Schmidtea mediterranea mk4.034667.01  
Schmidtea mediterranea mk4.005704.00  
Schmidtea mediterranea mk4.004013.03  
Trypanosoma brucei gambiense Tbg972.1.20   DNA-directed RNA polymerase III, putative
Trypanosoma brucei gambiense Tbg972.4.3880   DNA-directed RNA polymerase II subunit 2, putative
Trypanosoma brucei Tb927.4.3810   DNA-directed RNA polymerase II subunit 2, putative
Trypanosoma brucei Tb927.1.540   DNA-directed RNA polymerase III, putative
Trypanosoma congolense TcIL3000_0_29100   DNA-directed RNA polymerase II subunit 2, putative
Trypanosoma congolense TcIL3000_1_120   DNA-directed RNA polymerase III, putative
Trypanosoma congolense TcIL3000_0_32940   DNA-directed RNA polymerase II subunit 2, putative
Trypanosoma cruzi TcCLB.511417.40   DNA-directed RNA polymerase III, putative
Trypanosoma cruzi TcCLB.505997.210   DNA-directed RNA polymerase III subunit, putative
Toxoplasma gondii TGME49_258210   DNA-directed RNA polymerase II RPB2
Toxoplasma gondii TGME49_272740   DNA-directed RNA polymerase III RPC2
Theileria parva TP04_0340   DNA-directed RNA polymerase II subunit, putative
Theileria parva TP03_0746   DNA-directed RNA polymerase III subunit, putative
Trichomonas vaginalis TVAG_117450   DNA-directed RNA polymerase I subunit, putative
Trichomonas vaginalis TVAG_379530   DNA-directed RNA polymerase III subunit, putative

Essentiality

PF3D7_0215700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.3810 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.4.3810 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.4.3810 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.4.3810 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.1.540 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.1.540 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.1.540 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.1.540 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C26E6.4 Caenorhabditis elegans adult lethal wormbase
CELE_C26E6.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_C26E6.4 Caenorhabditis elegans larval lethal wormbase
CELE_C26E6.4 Caenorhabditis elegans slow growth wormbase
CELE_C26E6.4 Caenorhabditis elegans sterile wormbase
CELE_F09F7.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_F09F7.3 Caenorhabditis elegans larval arrest wormbase
CELE_F09F7.3 Caenorhabditis elegans larval lethal wormbase
CELE_F09F7.3 Caenorhabditis elegans slow growth wormbase
CELE_F09F7.3 Caenorhabditis elegans sterile wormbase
YOR207C Saccharomyces cerevisiae inviable yeastgenome
YOR151C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0312400 Plasmodium berghei Slow plasmo
PBANKA_0605200 Plasmodium berghei Essential plasmo
TGME49_258210 Toxoplasma gondii Probably essential sidik
TGME49_272740 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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
  • 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.
  • 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
  • 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
  • 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

Druggability index (range: 0 to 1): 0.8

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.

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Gene identifier PF3D7_0215700 (Plasmodium falciparum), DNA-directed RNA polymerase II subunit RPB2, putative
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