Detailed view for PF3D7_1117100

Basic information

TDR Targets ID: 1646
Plasmodium falciparum, deubiquinating/deneddylating enzyme
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 5.3564 | Length (AA): 465 | MW (Da): 54460 | Paralog Number: 0

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

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

PF01088   Ubiquitin carboxyl-terminal hydrolase, family 1

Gene Ontology

Mouse over links to read term descriptions.
GO:0004843   ubiquitin-specific protease activity  
GO:0005622   intracellular  
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 7 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
12 334 1cmx (A) 8 234 21.00 0 1 0.22 0.18
64 274 1xd3 (A) 6 223 16.00 0 0.85 0.66 -0.49
10 460 4wlr (A) 6 318 36.00 0 1 0.729292 1.15
301 463 4uos (A) 2 172 19.00 0.71 0.29 0.548538 -0.62
10 462 4wlr (A) 6 318 36.00 0 1 0.736621 0.95
12 385 4ig7 (A) 6 261 37.00 0 1 0.453457 0.99
280 459 4uos (A) 1 180 15.00 0.6 0.16 0.621539 -1.31

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 - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, early schizont, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, early trophozoite, late ring, late schizont, late trophozoite, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Ring, Sporozoite. Zanghi G
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_128387)

Species Accession Gene Product
Arabidopsis thaliana AT5G16310   ubiquitin thiolesterase UCH1
Arabidopsis thaliana AT1G65650   peptidase C12, ubiquitin carboxyl-terminal hydrolase 2
Brugia malayi Bm1_20630   ubiquitin C-terminal hydrolase UCH-L5
Candida albicans CaO19.3930   ubiquitin carboxyl-terminal hydrolase-like protein
Candida albicans CaO19.11412   ubiquitin carboxyl-terminal hydrolase-like protein
Caenorhabditis elegans CELE_C08B11.7   Protein UBH-4
Cryptosporidium hominis Chro.10139   UCHL5 protein
Cryptosporidium parvum cgd1_1170   ubiquitin C-terminal hydrolase
Dictyostelium discoideum DDB_G0285527   peptidase C12 family protein
Drosophila melanogaster Dmel_CG3431   Ubiquitin carboxy-terminal hydrolase L5 ortholog
Drosophila melanogaster Dmel_CG1950   Uch-L5-related
Echinococcus granulosus EgrG_000143100   ubiquitin carboxyl terminal hydrolase isozyme
Entamoeba histolytica EHI_140500   ubiquitin carboxyl-terminal hydrolase, putative
Echinococcus multilocularis EmuJ_000141500   ubiquitin carboxyl terminal hydrolase isozyme
Echinococcus multilocularis EmuJ_000143100   ubiquitin carboxyl terminal hydrolase isozyme
Homo sapiens ENSG00000116750   ubiquitin carboxyl-terminal hydrolase L5
Leishmania braziliensis LbrM.24.0420   ubiquitin carboxyl-terminal hydrolase, putative,cysteine peptidase, Clan CA, family C12, putative
Leishmania donovani LdBPK_240420.1   ubiquitin carboxyl-terminal hydrolase, putative
Leishmania infantum LinJ.24.0420   ubiquitin carboxyl-terminal hydrolase, putative,cysteine peptidase, Clan CA, family C12, putative
Leishmania major LmjF.24.0420   ubiquitin carboxyl-terminal hydrolase, putative,cysteine peptidase, Clan CA, family C12, putative
Leishmania mexicana LmxM.24.0420   ubiquitin carboxyl-terminal hydrolase, putative,cysteine peptidase, Clan CA, family C12, putative
Loa Loa (eye worm) LOAG_13247   ubiquitin C-terminal hydrolase UCH-L5
Mus musculus ENSMUSG00000018189   ubiquitin carboxyl-terminal esterase L5
Neospora caninum NCLIV_063760   hypothetical protein
Oryza sativa 4331185   Os02g0822200
Oryza sativa 4328506   Os02g0180100
Plasmodium berghei PBANKA_0930900   deubiquinating/deneddylating enzyme, putative
Plasmodium falciparum PF3D7_1117100   deubiquinating/deneddylating enzyme
Plasmodium knowlesi PKNH_0914800   deubiquinating/deneddylating enzyme, putative
Plasmodium vivax PVX_091485   ubiquitin C-terminal hydrolase, family 1, putative
Plasmodium yoelii PY04400   ubiquitin carboxyl-terminal hydrolase isozyme l5
Schistosoma japonicum Sjp_0060830   ko:K05610 ubiquitin carboxyl-terminal hydrolase L5, putative
Schistosoma mansoni Smp_083200.2   ubiquitinyl hydrolase-UCH37 (C12 family)
Schistosoma mansoni Smp_083200.1   ubiquitinyl hydrolase-UCH37 (C12 family)
Schmidtea mediterranea mk4.000177.03  
Trypanosoma brucei gambiense Tbg972.11.5810   ubiquitin carboxyl-terminal hydrolase, putative,cysteine peptidase, Clan CA, family C12, putative
Trypanosoma congolense TcIL3000.11.5350   ubiquitin carboxyl-terminal hydrolase, putative
Trypanosoma cruzi TcCLB.510945.10   ubiquitin carboxyl-terminal hydrolase, putative
Trypanosoma cruzi TcCLB.419703.20   ubiquitin carboxyl-terminal hydrolase, putative
Toxoplasma gondii TGME49_247240   ubiquitin carboxyl-terminal hydrolase, family 1 protein

Essentiality

PF3D7_1117100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_C08B11.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_C08B11.7 Caenorhabditis elegans larval arrest wormbase
PBANKA_0930900 Plasmodium berghei Slow plasmo
TGME49_247240 Toxoplasma gondii Probably non-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
  • 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.
  • 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
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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

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
Homo sapiens ubiquitin carboxyl-terminal hydrolase L5 Compounds References
Leishmania major ubiquitin carboxyl-terminal hydrolase, putative,cysteine peptidase, Clan CA, family C12, putative 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
0.0313 0.3034 0
0.0092 0.3002 0.4319
0.008 0.3002 0.4319
0.0313 0.3034 0
0.009 0.3002 0.4319
0.0303 0.3177 0.3156
0.0099 0.3002 0.4319
0.0313 0.3034 0
0.007 0.3002 0.4319
0.0303 0.3177 0.3156
0.0313 0.3034 0
0.0099 0.3002 0.4319
0.0298 0.2906 0
0.0313 0.3034 0
0.0298 0.2906 0
0.0313 0.3034 0
0.0089 0.3002 0.4319
0.0125 0.3038 0.3038
0.0077 0.3002 0.4319

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.

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Gene identifier PF3D7_1117100 (Plasmodium falciparum), deubiquinating/deneddylating enzyme
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