Detailed view for PF3D7_0413900

Basic information

TDR Targets ID: 3906
Plasmodium falciparum, ubiquitin carboxyl-terminal hydrolase 13, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 4.9686 | Length (AA): 853 | MW (Da): 98471 | 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

PF00443   Ubiquitin carboxyl-terminal hydrolase
PF02148   Zn-finger in ubiquitin-hydrolases and other protein
PF09288   Fungal ubiquitin-associated 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:0000502   proteasome complex  
GO:0008270   zinc ion binding  
GO:0005515   protein binding  
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 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
166 289 2g45 (A) 175 289 48.00 0.0000000017 1 0.57 0.38
726 786 2dak (A) 2 62 26.00 0.000011 0.56 0.49 -1.16
1 853 3ihp (A) 1 834 28.00 0 1 0.9506 1.35
168 289 2l80 (A) 2 114 47.00 0 1 0.632625 -0.18
717 771 1wiv (A) 13 67 24.00 0.52 0.97 0.419078 -0.26

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 - 32 hs, Oocyst. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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, Ring, Female Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Sporozoite, Male Gametocyte. Zanghi G Lasonder E
Show/Hide expression data references
  • 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.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.

Orthologs

Ortholog group members (OG5_127550)

Species Accession Gene Product
Arabidopsis thaliana AT3G20630   ubiquitin carboxyl-terminal hydrolase 14
Babesia bovis BBOV_IV004350   ubiquitin carboxyl-terminal hydrolase, putative
Brugia malayi Bm1_56725   Ubiquitin carboxyl-terminal hydrolase family protein
Candida albicans CaO19.9091   ubiquitin hydrolase
Candida albicans CaO19.1516   ubiquitin hydrolase
Caenorhabditis elegans CELE_T27A3.2   Protein USP-5
Cryptosporidium hominis Chro.60521   ubiquitin-specific protease
Cryptosporidium parvum cgd6_4550   UBP_znfinger+UBA; UBP5 like deubiquitinating enzyme with a UB hydrolase domain and two UBA domains at the C-terminus
Dictyostelium discoideum DDB_G0291239   UBP-type zinc finger-containing protein
Drosophila melanogaster Dmel_CG12082   CG12082 gene product from transcript CG12082-RB
Echinococcus granulosus EgrG_000095700   ubiquitin carboxyl terminal hydrolase 5
Echinococcus granulosus EgrG_002006000   ubiquitin carboxyl terminal hydrolase 5
Echinococcus granulosus EgrG_002058800   ubiquitin carboxyl terminal hydrolase 5
Entamoeba histolytica EHI_049940   ubiquitin carboxyl-terminal hydrolase 5, putative
Echinococcus multilocularis EmuJ_000095700   ubiquitin carboxyl terminal hydrolase 5
Giardia lamblia GL50803_102710   Ubiquitin carboxyl-terminal hydrolase 14
Homo sapiens ENSG00000111667   ubiquitin specific peptidase 5 (isopeptidase T)
Homo sapiens ENSG00000058056   ubiquitin specific peptidase 13 (isopeptidase T-3)
Leishmania braziliensis LbrM.29.2270   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Leishmania donovani LdBPK_292410.1   ubiquitin carboxyl-terminal hydrolase, putative
Leishmania infantum LinJ.29.2410   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Leishmania major LmjF.29.2300   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Leishmania mexicana LmxM.08_29.2300   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Loa Loa (eye worm) LOAG_07416   ubiquitin carboxyl-terminal hydrolase
Loa Loa (eye worm) LOAG_15837   hypothetical protein
Mus musculus 72607   ubiquitin specific peptidase 13 (isopeptidase T-3)
Mus musculus ENSMUSG00000038429   ubiquitin specific peptidase 5 (isopeptidase T)
Neospora caninum NCLIV_013610   Ubiquitin carboxyl-terminal hydrolase (EC 3.1.2.15), related
Neospora caninum NCLIV_013620   Ubiquitin carboxyl-terminal hydrolase (EC 3.1.2.15), related
Plasmodium berghei PBANKA_0715900   ubiquitin carboxyl-terminal hydrolase 13, putative
Plasmodium falciparum PF3D7_0413900   ubiquitin carboxyl-terminal hydrolase 13, putative
Plasmodium knowlesi PKNH_0505500   ubiquitin carboxyl-terminal hydrolase 13, putative
Plasmodium vivax PVX_089655   ubiquitin carboxyl-terminal hydrolase 13, putative
Plasmodium yoelii PY00546   ubiquitin specific protease 5
Saccharomyces cerevisiae YBR058C   Ubp14p
Schistosoma japonicum Sjp_0208460   ko:K01072 ubiquitin thiolesterase [EC3.1.2.15], putative
Schistosoma mansoni Smp_069960   ubiquitin-specific peptidase 5 (C19 family)
Schmidtea mediterranea mk4.001723.07   Ubiquitin carboxyl-terminal hydrolase
Trypanosoma brucei gambiense Tbg972.3.5420   ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative
Trypanosoma brucei Tb927.3.4840   ubiquitin carboxyl-terminal hydrolase, putative
Trypanosoma congolense TcIL3000_0_42590   ubiquitin carboxyl-terminal hydrolase, putative
Trypanosoma cruzi TcCLB.508185.19   cysteine peptidase, Clan CA, family C19, putative
Trypanosoma cruzi TcCLB.510325.10   cysteine peptidase, Clan CA, family C19, putative
Trypanosoma cruzi TcCLB.508153.120   ubiquitin carboxyl-terminal hydrolase, putative
Toxoplasma gondii TGME49_213870   UBA/TS-N domain-containing protein
Theileria parva TP01_0316   ubiquitin carboxyl-terminal hydrolase a, putative
Trichomonas vaginalis TVAG_029150   Clan CA, family C19, ubiquitin hydrolase-like cysteine peptidase

Essentiality

PF3D7_0413900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.4840 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.3.4840 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.3.4840 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.3.4840 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_T27A3.2 Caenorhabditis elegans slow growth wormbase
TGME49_213870 Toxoplasma gondii Probably 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 specific peptidase 5 (isopeptidase T) Compounds References
Leishmania major ubiquitin hydrolase, putative,cysteine peptidase, Clan CA, family C19, putative Compounds References
Homo sapiens ubiquitin specific peptidase 13 (isopeptidase T-3) 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
0.0004 0.5 0.5
0.0004 0.5 0.5
0.0042 0.2957 0.2957
0.0003 0.5 0.5
0.0004 0.5 0.5
0.0024 0.889 1

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_0413900 (Plasmodium falciparum), ubiquitin carboxyl-terminal hydrolase 13, putative
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