Detailed view for PF3D7_1345500

Basic information

TDR Targets ID: 139
Plasmodium falciparum, ubiquitin-conjugating enzyme E2
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.1307 | Length (AA): 278 | MW (Da): 32788 | Paralog Number: 1

Signal peptide: Y | GPI Anchor: N | Predicted trans-membrane segments: 1

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

PF00179   Ubiquitin-conjugating enzyme

Gene Ontology

Mouse over links to read term descriptions.
GO:0019787   small conjugating protein ligase activity  
GO:0051246   regulation of protein metabolic process  
GO:0043687   post-translational protein modification  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
117 249 2h2y (A) 3 135 99.99 0 1 1.74 -2.38
126 277 2e2c () 22 171 26.00 0 1 1.04 -1.58
138 245 1y6l (A) 5 111 39.00 0 1 1.13 -2.64
107 275 4r8p (L) 91 340 28.00 0.00000000038 1 0.990214 -0.41
117 249 2h2y (A) 3 135 99.99 0 1 1.77282 -2.04

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:

PDB tag
  • 2FO3:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2H2Y:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 32 hs, early schizont, Oocyst, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, gametocyte, early trophozoite, late schizont, late trophozoite, Ring, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Sporozoite. Zanghi G
Show/Hide expression data references
  • 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
  • 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_128794)

Species Accession Gene Product
Arabidopsis thaliana AT1G75440   putative ubiquitin-conjugating enzyme E2 16
Arabidopsis thaliana AT1G45050   ubiquitin-conjugating enzyme 15
Arabidopsis thaliana AT5G42990   ubiquitin-conjugating enzyme 18
Babesia bovis BBOV_II006740   ubiquitin-conjugating enzyme E2
Brugia malayi Bm1_47885   ubiquitin-conjugating enzyme UBC2-1 - Arabidopsis thaliana
Candida albicans CaO19.12797   ubiquitin-conjugating enzyme
Candida albicans CaO19.5337   ubiquitin-conjugating enzyme
Caenorhabditis elegans CELE_Y54E5B.4   Protein UBC-16
Dictyostelium discoideum DDB_G0268938   ubiquitin-conjugating enzyme E2W
Drosophila melanogaster Dmel_CG7220   CG7220 gene product from transcript CG7220-RA
Homo sapiens ENSG00000104343   ubiquitin-conjugating enzyme E2W (putative)
Loa Loa (eye worm) LOAG_02096   hypothetical protein
Mus musculus ENSMUSG00000025939   ubiquitin-conjugating enzyme E2W (putative)
Neospora caninum NCLIV_027420   hypothetical protein
Neospora caninum NCLIV_001990   Ubiquitin carrier protein (EC 6.3.2.-), related
Oryza sativa 4333728   Os03g0681400
Oryza sativa 4352894   Os12g0636800
Plasmodium berghei PBANKA_1358400   ubiquitin-conjugating enzyme E2, putative
Plasmodium berghei PBANKA_1029700   ubiquitin-conjugating enzyme E2, putative
Plasmodium falciparum PF3D7_1345500   ubiquitin-conjugating enzyme E2
Plasmodium falciparum PF3D7_1412900   ubiquitin-conjugating enzyme E2, putative
Plasmodium knowlesi PKNH_1255800   ubiquitin-conjugating enzyme E2, putative
Plasmodium knowlesi PKNH_1345400   ubiquitin-conjugating enzyme E2, putative
Plasmodium vivax PVX_083175   ubiquitin-conjugating enzyme E2, putative
Plasmodium vivax PVX_085810   ubiquitin-conjugating enzyme, putative
Plasmodium yoelii PY05644   putative ubiquitin-conjugating enzyme 16
Plasmodium yoelii PY00590   putative ubiquitin-conjugating enzyme 16
Toxoplasma gondii TGME49_259090   ubiquitin-conjugating enzyme subfamily protein
Toxoplasma gondii TGME49_295990   ubiquitin conjugating enzyme E2, putative
Theileria parva TP02_0640   ubiquitin-protein ligase, putative

Essentiality

PF3D7_1345500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1029700 Plasmodium berghei Dispensable plasmo
PBANKA_1358400 Plasmodium berghei Essential plasmo
TGME49_295990 Toxoplasma gondii Essentiality uncertain sidik
TGME49_259090 Toxoplasma gondii Essentiality uncertain sidik
TGME49_295990 Toxoplasma gondii Probably essential sidik
TGME49_259090 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • 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

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
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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User comments

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Gene identifier PF3D7_1345500 (Plasmodium falciparum), ubiquitin-conjugating enzyme E2
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