Detailed view for PF3D7_0904600

Basic information

TDR Targets ID: 4723
Plasmodium falciparum, ubiquitin specific protease, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.0516 | Length (AA): 1770 | MW (Da): 207568 | Paralog Number: 0

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

PF00443   Ubiquitin carboxyl-terminal hydrolase
PF06337   DUSP domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0036459   GO:thiol-dependent ubiquitinyl hydrolase activity  

GO:0016579   protein deubiquitination  
GO:0004843   ubiquitin-specific protease activity  
GO:0004221   ubiquitin thiolesterase activity  
GO:0006511   ubiquitin-dependent protein catabolic process  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 18 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
1406 1770 2f1z (A) 205 521 21.00 0 1 0.16 0.7
1410 1769 2gfo (A) 772 1108 26.00 0 1 0.39 -0.35
8 104 4u5a (C) 115 238 30.00 0.33 0.25 0.256702 -0.11
52 830 3vuo (A) 231 1105 24.00 0.00065 0.99 0.399813 1.46
432 488 3lmn (A) 26 91 28.00 0.82 0.43 0.122203 0.57
587 1229 4om9 (A) 76 888 24.00 0.7 0.9 0.253977 1.26
843 930 3ult (A) 12 103 27.00 0.089 0.04 0.555418 -2.85
931 1029 4ux3 (A) 173 1004 31.00 0.51 0.06 0.343632 -0.65
1407 1767 4fk5 (A) 129 465 32.00 0.0000000000055 1 0.287655 0.63
1407 1767 3mhs (A) 129 465 33.00 0 1 0.313655 0.67
1530 1768 2y6e (A) 381 921 31.00 0.00000004 1 0.294728 0.87
8 105 4u5a (C) 115 239 30.00 0.41 0.16 0.245245 -0.19
52 818 3vuo (A) 231 1105 25.00 0.00092 0.98 0.391991 1.49
153 430 4u0r (A) 160 496 21.00 0.013 0.61 0.384634 -0.51
823 920 3ult (A) 9 110 28.00 0.062 0.07 0.548445 -2.59
921 1019 4ux3 (A) 173 1004 31.00 0.5 0.06 0.344014 -0.65
1366 1755 4w4u (D) 83 465 33.00 0.000000047 1 0.154543 1.14
1518 1756 2y6e (A) 381 921 31.00 0.000000039 1 0.29565 0.87

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 Male Gametocyte. Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Oocyst, Ring, Sporozoite, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte. Otto TD PlasmoDB
Show/Hide expression data references
  • 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.
  • 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_163015)

Species Accession Gene Product
Plasmodium berghei PBANKA_0416800   ubiquitin specific protease, putative
Plasmodium falciparum PF3D7_0904600   ubiquitin specific protease, putative
Plasmodium knowlesi PKNH_0702300   ubiquitin specific protease, putative
Plasmodium vivax PVX_098675   ubiquitin carboxyl-terminal hydrolase, putative
Plasmodium yoelii PY04608   Ubiquitin carboxyl-terminal hydrolase family 2, putative

Essentiality

PF3D7_0904600 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0416800 Plasmodium berghei Dispensable plasmo
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
  • 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0004 0.5 0.5
0.0004 0.5 0.5
0.0003 0.5 0.5
0.0004 0.5 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.

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_0904600 (Plasmodium falciparum), ubiquitin specific protease, putative
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