Detailed view for PF3D7_0316900

Basic information

TDR Targets ID: 3666
Plasmodium falciparum, E3 ubiquitin-protein ligase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.9125 | Length (AA): 600 | MW (Da): 71009 | Paralog Number: 0

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

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

PF13920   Zinc finger, C3HC4 type (RING finger)

Gene Ontology

Mouse over links to read term descriptions.
GO:0008270   zinc ion binding  
GO:0005515   protein binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 14 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
192 488 2aqw (A) 4 318 19.00 0.000027 0.15 0.54 -0.01
542 589 1chc () 6 55 29.00 0.0000087 1 0.39 -0.12
152 344 4v3d (A) 507 716 18.00 0.24 0.07 0.441767 -0.15
536 585 2ecn (A) 10 59 42.00 0.53 0.68 0.375433 0.84
538 593 4auq (B) 246 298 28.00 0.38 0.97 0.400533 -0.14
543 581 2d8t (A) 17 56 41.00 0.37 0.89 0.4129 0.72
544 586 4r7e (A) 648 692 37.00 0.55 0.97 0.354567 0.85
544 580 2yur (A) 18 58 38.00 0.73 0.94 0.419567 0.07
106 206 5c7c (A) 253 351 7.00 0.000015 0.01 0.208514 -0.11
533 592 4auq (B) 242 298 25.00 0.37 0.71 0.337067 0.12
540 584 2ecn (A) 15 59 49.00 0.0085 0.64 0.369825 1.61
542 580 2d8t (A) 17 56 41.00 0.38 0.89 0.413809 0.72
543 585 4r7e (A) 648 692 37.00 0.57 0.97 0.355486 0.85
543 579 2yur (A) 18 58 38.00 0.75 0.94 0.42047 0.07

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 - 40 hs, intra-erythrocytic - 48 hs, gametocyte, merozoite, sporozoite, early ring, early schizont, late ring, late schizont. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 32 hs, early trophozoite, late trophozoite, Ring, Sporozoite, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Oocyst. Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Male Gametocyte. Lasonder E
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.
  • 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_144867)

Species Accession Gene Product
Babesia bovis BBOV_I004370   conserved hypothetical protein
Cryptosporidium hominis Chro.40155   C0740c
Cryptosporidium parvum cgd4_1360   ring domain containing protein
Plasmodium berghei PBANKA_0808300   E3 ubiquitin-protein ligase, putative
Plasmodium falciparum PF3D7_0316900   E3 ubiquitin-protein ligase, putative
Plasmodium knowlesi PKNH_0824900   E3 ubiquitin-protein ligase, putative
Plasmodium vivax PVX_095385   E3 ubiquitin-protein ligase, putative
Plasmodium yoelii PY05143   putative zinc-finger protein
Theileria parva TP01_1022   zinc finger protein, putative

Essentiality

PF3D7_0316900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0808300 Plasmodium berghei Essential plasmo
Show/Hide essentiality data references
  • 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.
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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

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.

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_0316900 (Plasmodium falciparum), E3 ubiquitin-protein ligase, putative
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