Detailed view for PF3D7_API04400

Basic information

TDR Targets ID: 322068
Plasmodium falciparum, DNA-directed RNA polymerase subunit beta, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.0319 | Length (AA): 1024 | MW (Da): 122186 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 5

Druggability Group : DG4

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
PF04565   RNA polymerase Rpb2, domain 3

Gene Ontology

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

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 3 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
5 1019 2a6h (C) 9 1116 22.00 0 1 0.597611 2.06
11 1019 2a6h (C) 18 1116 22.00 0 1 1.03315 1.7
157 269 4ux7 (A) 68 208 35.00 0.66 0.19 -0.0670484 2.52

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 60-80% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, Oocyst, Ring, Sporozoite, Female Gametocyte, Male Gametocyte. Otto TD Zanghi G Lasonder E
Show/Hide expression data references
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • 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.

Orthologs

Ortholog group members (OG5_130697)

Species Accession Gene Product
Arabidopsis thaliana ArthCp014   RNA polymerase beta chain
Babesia bovis BBOV_V000130   rpoB
Chlamydia trachomatis CT_315   DNA-directed RNA polymerase subunit beta
Escherichia coli b3987   RNA polymerase, beta subunit
Mycobacterium leprae ML1891c   DNA-DIRECTED RNA POLYMERASE (BETA CHAIN) RPOB (TRANSCRIPTASE BETA CHAIN) (RNA POLYMERASE BETA SUBUNIT)
Mycobacterium tuberculosis Rv0667   DNA-directed RNA polymerase (beta chain) RpoB (transcriptase beta chain) (RNA polymerase beta subunit)
Mycobacterium ulcerans MUL_0746   DNA-directed RNA polymerase subunit beta
Oryza sativa 3131432   RNA polymerase beta chain
Oryza sativa 9267308   Os02g0443000
Oryza sativa 9266573   Os04g0240100
Oryza sativa 3131434   RNA polymerase beta'' subunit
Plasmodium berghei PBANKA_API00150   DNA-directed RNA polymerase subunit beta, putative
Plasmodium falciparum PF3D7_API04400   DNA-directed RNA polymerase subunit beta, putative
Plasmodium knowlesi PKNH_API05300   DNA-directed RNA polymerase subunit beta, putative
Schmidtea mediterranea mk4.049882.01  
Treponema pallidum TP0241   DNA-directed RNA polymerase subunit beta
Theileria parva TP05_0028   DNA-directed RNA polymerase beta chain, putative
Wolbachia endosymbiont of Brugia malayi Wbm0647   DNA-directed RNA polymerase subunit beta/beta'

Essentiality

PF3D7_API04400 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b3987 Escherichia coli essential goodall
Show/Hide essentiality data references
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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
Species Known druggable target Linked compounds Reference
Escherichia coli RNA polymerase, beta subunit Compounds References
Mycobacterium leprae DNA-DIRECTED RNA POLYMERASE (BETA CHAIN) RPOB (TRANSCRIPTASE BETA CHAIN) (RNA POLYMERASE BETA SUBUNIT) Compounds References
Mycobacterium tuberculosis DNA-directed RNA polymerase (beta chain) RpoB (transcriptase beta chain) (RNA polymerase beta subunit) Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0496 0.5932 1
0.1236 1 1
0.125 0.2893 1
0.0496 0.8058 1
0.0585 0.4675 1
0.047 0.2588 1
0.0473 0.2587 1
0.0449 0.2683 1
0.047 0.259 1
0.1027 1 1
0.0496 0.6087 1
0.124 1 1
0.1811 1 0.5
0.0487 0.2997 1
0.0841 0.5 0.5
0.0496 0.6087 1
0.0455 0.2607 1
0.1235 0.2513 1
0.0466 0.2575 1
0.0415 0.5234 0.5
0.1246 1 0.5
0.158 1 1
0.0488 0.5874 1
0.0827 0.2673 1
0.0479 0.3606 1
0.0475 0.2597 1
0.0453 0.2942 1
0.0893 0.255 1
0.2086 1 0.5
0.0415 0.5234 0.5
0.125314 0.545419 1
0.2995 1 0.5
0.0893 0.255 1
0.084 0.3897 1
0.2531 1 1
0.1668 1 1
0.0496 1 0.5
0.1794 1 1
0.0863 0.3207 1
0.2531 1 1
0.1369 1 1
0.1246 1 0.5
0.2531 1 1
0.1671 0.5887 1
0.125 0.2893 1
0.1773 1 1
0.0475 0.2597 1
0.0424 0.4279 0.5
0.0471 0.2996 1
0.0872 0.4083 1
0.1258 0.7572 1
0.0488 0.5874 1
0.1186 1 1
0.2531 1 1
0.0848 0.3966 1
0.1804 1 0.5
0.0479 0.3606 1
0.0931 1 0.5
0.0463 0.2539 1
0.0221 0.2529 1
0.0465 0.2571 1
0.047 0.259 1
0.0476 0.5556 0.5
0.1235 0.2513 1
0.0836 1 0.5
0.1369 1 1
0.0449 0.2683 1
0.0496 0.5 0.5
0.0295 0.2571 1
0.0496 0.5 0.5
0.2086 1 0.5
0.047 0.259 1
0.0893 0.255 1
0.2086 1 0.5
0.0848 1 1
0.1842 1 1
0.1668 1 1
0.0466 0.2581 1
0.0832 1 0.5
0.0424 0.4279 0.5
0.0453 0.2934 1
0.0865 0.9331 1
0.084 0.3897 1
0.2531 1 1
0.0221 0.2529 1
0.0856 0.8715 1
0.0496 0.5932 1
0.0466 0.2592 1
0.0471 0.2996 1
0.0479 0.2598 1
0.0483 0.2558 1
0.084 0.3897 1
0.0476 0.5556 0.5
0.0414 1 0.5
0.084 0.3897 1
0.047 0.259 1
0.2531 1 1
0.0466 0.2584 1
0.0477 0.2599 1
0.0534189 0.549259 1
0.1668 1 1
0.0893 0.255 1
0.0289 0.3389 1
0.1668 1 1
0.0414 1 0.5
0.1556 0.4678 1
0.0842 1 0.5
0.2531 1 1
0.0475 0.2593 1
0.0479 0.3606 1
0.2531 1 1
0.1323 1 0.5

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_API04400 (Plasmodium falciparum), DNA-directed RNA polymerase subunit beta, putative
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