Detailed view for PF3D7_1245300

Basic information

TDR Targets ID: 5489
Plasmodium falciparum, NEDD8-conjugating enzyme UBC12, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 4.5991 | Length (AA): 157 | MW (Da): 18401 | Paralog Number: 0

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

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:0005575   cellular_component  
GO:0019787   small conjugating protein ligase activity  
GO:0051246   regulation of protein metabolic process  
GO:0043687   post-translational protein modification  

Metabolic Pathways

Ubiquitin mediated proteolysis (KEGG)

Structural information

Modbase 3D models:

There are 8 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
3 156 1yh2 (A) 5 160 25.00 0 1 1.35 -1.19
6 157 1y8x (A) 25 176 34.00 0 1 1.55 -1.76
14 133 1zdn (A) 15 136 30.00 0.0000000000016 1 1.32 -2.05
2 146 3o2u (A) 1019 1169 38.00 0.0000034 1 1.48527 -1.29
2 156 2edi (A) 6 169 26.00 0.000019 1 1.30406 -0.14
4 150 2nvu (C) 23 169 35.00 0.0000000000055 1 1.50101 -1.22
57 117 2fo3 (A) 55 116 30.00 0.00031 0.93 0.735735 0.25
60 123 1uzx (A) 83 158 41.00 0.026 0.71 0.662843 0.75

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, Male Gametocyte. Otto TD Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 24 hs, early schizont, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile early trophozoite, late trophozoite, Ring, Sporozoite. PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 8 hs, Female Gametocyte. Otto TD Lasonder E
Show/Hide expression data references
  • 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.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • 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_128611)

Species Accession Gene Product
Arabidopsis thaliana AT2G18600   ubiquitin-conjugating enzyme family protein
Arabidopsis thaliana AT4G36800   RUB1 conjugating enzyme 1
Babesia bovis BBOV_IV009300   hypothetical protein
Candida albicans CaO19.12866   potential ubiquitin-like protein-conjugating E2 enzyme similar to S. cerevisiae UBC12 (YLR306W) which acts in Rub1-conjugation,
Candida albicans CaO19.5411   potential ubiquitin-like protein-conjugating E2 enzyme similar to S. cerevisiae UBC12 (YLR306W) which acts in Rub1-conjugation,
Cryptosporidium hominis Chro.80032   ubiquitin-conjugating enzyme e2
Cryptosporidium parvum cgd8_220   ubiquitin-conjugating enzyme e2
Dictyostelium discoideum DDB_G0281725   NEDD8-conjugating enzyme
Drosophila melanogaster Dmel_CG7375   Ubiquitin conjugating enzyme 12
Echinococcus granulosus EgrG_000650820   Ubiquitin carrier protein
Echinococcus granulosus EgrG_001154600   UBiquitin Conjugating enzyme family member
Echinococcus granulosus EgrG_002060100   3'partial|hypothetical protein
Entamoeba histolytica EHI_003010   ubiquitin-conjugating enzyme family protein
Echinococcus multilocularis EmuJ_000351600  
Echinococcus multilocularis EmuJ_001154600   UBiquitin Conjugating enzyme family member
Echinococcus multilocularis EmuJ_000650820   Ubiquitin carrier protein
Echinococcus multilocularis EmuJ_000503220   protein kinase
Homo sapiens ENSG00000130725   ubiquitin-conjugating enzyme E2M
Mus musculus ENSMUSG00000005575   ubiquitin-conjugating enzyme E2M
Neospora caninum NCLIV_019430   Ubiquitin carrier protein (EC 6.3.2.-), related
Oryza sativa 4345411   Os08g0374100
Oryza sativa 4346713   Os09g0321900
Oryza sativa 4348232   Os10g0190000
Plasmodium berghei PBANKA_1458500   NEDD8-conjugating enzyme UBC12, putative
Plasmodium falciparum PF3D7_1245300   NEDD8-conjugating enzyme UBC12, putative
Plasmodium knowlesi PKNH_1465000   NEDD8-conjugating enzyme UBC12, putative
Saccharomyces cerevisiae YLR306W   NEDD8-conjugating protein UBC12
Schmidtea mediterranea mk4.001373.00   NEDD8-conjugating enzyme Ubc12
Toxoplasma gondii TGME49_280760   RUB1 conjugating enzyme
Theileria parva TP01_0844   ubiquitin-protein ligase, putative
Trichomonas vaginalis TVAG_038060   ubiquitin-conjugating enzyme E2-25kD, putative
Trichomonas vaginalis TVAG_497140   ubiquitin-conjugating enzyme rad6, putative
Trichomonas vaginalis TVAG_074860   ubiquitin-conjugating enzyme E2-25kD, putative
Trichomonas vaginalis TVAG_038730   nedd8-conjugating enzyme nce2, putative

Essentiality

PF3D7_1245300 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
TGME49_280760 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.

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

1 literature reference was collected for this gene.

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_1245300 (Plasmodium falciparum), NEDD8-conjugating enzyme UBC12, putative
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