Detailed view for Rv3579c

Basic information

TDR Targets ID: 9196
Mycobacterium tuberculosis, Possible tRNA/rRNA methyltransferase
Source Database / ID:  Tuberculist 

pI: 11.3642 | Length (AA): 322 | MW (Da): 34010 | 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

PF00588   SpoU rRNA Methylase family
PF08032   RNA 2'-O ribose methyltransferase substrate binding

Gene Ontology

Mouse over links to read term descriptions.
GO:0008173   RNA methyltransferase activity  
GO:0008168   methyltransferase activity  
GO:0003723   RNA binding  
GO:0006396   RNA processing  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 3 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
38 316 3nk6 (A) 2 273 29.00 0 1 1.13976 -0.01
67 307 1gz0 (A) 2 242 39.00 0 1 1.25045 -0.4
139 320 1zjr (A) 7 191 27.00 0 1 0.923517 -0.83

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
Lower 20-40% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. murphy
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_128345)

Species Accession Gene Product
Arabidopsis thaliana AT2G19870   tRNA/rRNA methyltransferase (SpoU) family protein
Brugia malayi Bm1_29705   ShTK domain containing protein
Candida albicans CaO19.182   potential methylase similar to S. cerevisiae PET56 (YOR201C) mitochondrial ribosomal RNA methylase
Candida albicans CaO19.7812   potential methylase similar to S. cerevisiae PET56 (YOR201C) mitochondrial ribosomal RNA methylase
Caenorhabditis elegans CELE_Y45F3A.9   Protein Y45F3A.9
Caenorhabditis elegans CELE_Y45F3A.8   Protein Y45F3A.8
Dictyostelium discoideum DDB_G0277479   hypothetical protein
Escherichia coli b4180   23S rRNA mG2251 2'-O-ribose methyltransferase, SAM-dependent
Echinococcus granulosus EgrG_000916610   ribosomal RNA methyltransferase, putative
Echinococcus multilocularis EmuJ_000916610   rrna methyltransferase 1 mitochondrial
Homo sapiens ENSG00000278619   mitochondrial rRNA methyltransferase 1 homolog (S. cerevisiae)
Loa Loa (eye worm) LOAG_08673   hypothetical protein
Mycobacterium leprae ML0324   Possible tRNA/rRNA methyltransferase
Mus musculus ENSMUSG00000018405   mitochondrial rRNA methyltransferase 1 homolog (S. cerevisiae)
Mycobacterium tuberculosis Rv3579c   Possible tRNA/rRNA methyltransferase
Mycobacterium ulcerans MUL_4155   tRNA/rRNA methyltransferase
Oryza sativa 4326542   Os01g0742000
Plasmodium berghei PBANKA_0315000   apicoplast RNA methyltransferase precursor, putative
Plasmodium falciparum PF3D7_0218300   apicoplast RNA methyltransferase precursor, putative
Plasmodium knowlesi PKNH_0402600   apicoplast RNA methyltransferase precursor, putative
Plasmodium vivax PVX_002625   rRNA methylase, putative
Plasmodium yoelii PY01246   rRNA methylase
Saccharomyces cerevisiae YOR201C   Mrm1p
Schistosoma japonicum Sjp_0033250   ko:K03218 RNA methyltransferase, TrmH family, putative
Schistosoma mansoni Smp_018480   rRNA methylase
Schmidtea mediterranea mk4.002975.01   Putative rrna methylase
Schmidtea mediterranea mk4.001109.03   Putative rrna methylase
Schmidtea mediterranea mk4.005907.00   Putative rrna methylase
Schmidtea mediterranea mk4.000658.07   Putative rrna methylase
Treponema pallidum TP0109   rRNA methylase
Wolbachia endosymbiont of Brugia malayi Wbm0489   rRNA methylase

Essentiality

Rv3579c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3641 this record Mycobacterium tuberculosis essential nmpdr
b4180 Escherichia coli non-essential goodall
PBANKA_0315000 Plasmodium berghei Dispensable plasmo
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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

63 literature references were 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 Rv3579c (Mycobacterium tuberculosis), Possible tRNA/rRNA methyltransferase
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