Detailed view for Tb927.11.10860

Basic information

TDR Targets ID: 18519
Trypanosoma brucei, 20S-pre-rRNA D-site endonuclease NOB1
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.079 | Length (AA): 432 | MW (Da): 47301 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | 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

PF08772   Nin one binding (NOB1) Zn-ribbon like
PF17146   PIN domain of ribonuclease

Gene Ontology

Mouse over links to read term descriptions.
GO:0042274   ribosomal small subunit biogenesis and assembly  
GO:0004521   endoribonuclease activity  
GO:0000469   cleavages during rRNA processing  

Metabolic Pathways

Ribosome biogenesis in eukaryotes (KEGG)

Structural information

Modbase 3D models:

There are 2 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
62 313 2lcq (A) 6 157 35.00 0 1 0.164633 1.34
275 348 2con (A) 7 79 34.00 0 0.4 0.339596 1.45

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 Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_128403)

Species Accession Gene Product
Arabidopsis thaliana AT5G41190   RNA-binding protein NOB1
Babesia bovis BBOV_IV004230   conserved hypothetical protein
Brugia malayi Bm1_41880   nin one binding protein
Candida albicans CaO19.6955   similar to Nin1 binding protein, chaperone of the 26S proteasome
Candida albicans CaO19.14217   similar to Nin1 binding protein, chaperone of the 26S proteasome
Caenorhabditis elegans CELE_Y54E10BR.4   Protein Y54E10BR.4
Cryptosporidium hominis Chro.70180   CG2972 gene product
Cryptosporidium parvum cgd7_1530   ART-4 protein; PIN+Zn ribbon domains. involved in RNA metabolism
Dictyostelium discoideum DDB_G0279821   hypothetical protein
Drosophila melanogaster Dmel_CG2972   CG2972 gene product from transcript CG2972-RB
Echinococcus granulosus EgrG_001130100   RNA binding protein NOB1
Entamoeba histolytica EHI_087710   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_001130100   RNA binding protein NOB1
Giardia lamblia GL50803_34141   Nin one binding protein-like protein
Homo sapiens ENSG00000141101   NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.35.5310   hypothetical protein, conserved
Leishmania donovani LdBPK_365290.1   Nin one binding (NOB1) Zn-ribbon like, putative
Leishmania infantum LinJ.36.5290   hypothetical protein, conserved
Leishmania major LmjF.36.5060   hypothetical protein, conserved
Leishmania mexicana LmxM.36.5060   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_05582   nin one binding protein
Mus musculus ENSMUSG00000003848   NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)
Neospora caninum NCLIV_061710   hypothetical protein, conserved
Oryza sativa 4328064   Os02g0114700
Plasmodium berghei PBANKA_0720800   RNA-binding protein NOB1, putative
Plasmodium falciparum PF3D7_0418700   RNA-binding protein NOB1, putative
Plasmodium knowlesi PKNH_0511400   RNA-binding protein NOB1, putative
Plasmodium vivax PVX_090025   RNA-binding protein NOB1, putative
Plasmodium yoelii PY05599   Drosophila melanogaster CG2972 gene product
Saccharomyces cerevisiae YOR056C   Nob1p
Schistosoma japonicum Sjp_0302360   ko:K07060 NOB1, LOC489733; NIN1/RPN12 binding protein 1 homolog, putative
Schistosoma mansoni Smp_064510   rna-binding protein nob1
Schmidtea mediterranea mk4.000363.04   RNA-binding protein NOB1
Trypanosoma brucei gambiense Tbg972.11.12170   hypothetical protein, conserved
Trypanosoma brucei Tb927.11.10860   20S-pre-rRNA D-site endonuclease NOB1
Trypanosoma congolense TcIL3000.11.11530   Nin one binding (NOB1) Zn-ribbon like, putative
Trypanosoma cruzi TcCLB.510423.40   Nin one binding (NOB1) Zn-ribbon like, putative
Toxoplasma gondii TGME49_218570   Nin one binding (NOB1) Zn-ribbon family protein
Theileria parva TP01_0331   hypothetical protein, conserved
Trichomonas vaginalis TVAG_151710   RNA-binding protein nob1, putative

Essentiality

Tb927.11.10860 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.2630 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.2630 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.2630 this record Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb11.01.2630 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y54E10BR.4 Caenorhabditis elegans larval arrest wormbase
CELE_Y54E10BR.4 Caenorhabditis elegans slow growth wormbase
YOR056C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0720800 Plasmodium berghei Essential plasmo
TGME49_218570 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • 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
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) normal (PATO:0000461) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) increased (PATO:0000470) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant gain of fitness) in procyclic forms . References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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.

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Gene identifier Tb927.11.10860 (Trypanosoma brucei), 20S-pre-rRNA D-site endonuclease NOB1
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