Detailed view for Rv0702

Basic information

TDR Targets ID: 7036
Mycobacterium tuberculosis, 50S ribosomal protein L4 RplD
Source Database / ID:  Tuberculist 

pI: 10.7786 | Length (AA): 223 | MW (Da): 23743 | 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

PF00573   Ribosomal protein L4/L1 family

Gene Ontology

Mouse over links to read term descriptions.
GO:0005840   ribosome  
GO:0005622   intracellular  
GO:0003735   structural constituent of ribosome  
GO:0006412   translation  

Metabolic Pathways

Ribosome (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
10 212 1dmg (A) 3 223 24.00 0.00003 1 0.772714 -0.1
11 208 4wfa (C) 4 200 43.00 0 1 1.32909 0.68
103 203 1dmg (A) 96 214 36.00 0.000028 1 0.822715 -1.16

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

Orthologs

Ortholog group members (OG5_127316)

Species Accession Gene Product
Arabidopsis thaliana AT1G07320   50S ribosomal protein L4
Arabidopsis thaliana AT2G20060   large subunit ribosomal protein L4
Babesia bovis BBOV_IV008840   50S ribosomal protein L4, putative
Brugia malayi Bm1_46425   ribosomal protein L4/L1 family protein
Candida albicans CaO19_7019   hypothetical protein
Candida albicans CaO19.7019   likely mitochondrial ribosomal protein similar to S. cerevisiae YML6 (YML025C) large subunit protein (E. coli L4)
Caenorhabditis elegans CELE_T23B12.2   Protein MRPL-4
Chlamydia trachomatis CT_527   50S ribosomal protein L4
Dictyostelium discoideum DDB_G0283275   hypothetical protein
Drosophila melanogaster Dmel_CG5818   mitochondrial ribosomal protein L4
Escherichia coli b3319   50S ribosomal subunit protein L4
Echinococcus granulosus EgrG_000520400   mitochondrial ribosomal protein L4
Echinococcus multilocularis EmuJ_000520400   mitochondrial ribosomal protein L4
Homo sapiens ENSG00000105364   mitochondrial ribosomal protein L4
Mycobacterium leprae ML1862c   PROBABLE 50S RIBOSOMAL PROTEIN L4 RPLD
Mus musculus ENSMUSG00000003299   mitochondrial ribosomal protein L4
Mycobacterium tuberculosis Rv0702   50S ribosomal protein L4 RplD
Mycobacterium ulcerans MUL_0791   50S ribosomal protein L4
Neospora caninum NCLIV_048820   50S ribosomal protein L4, putative
Oryza sativa 4350797   Os11g0585700
Oryza sativa 4332348   Os03g0265400
Plasmodium berghei PBANKA_0708800   mitochondrial ribosomal protein L4 precursor, putative
Plasmodium falciparum PF3D7_0822000   mitochondrial ribosomal protein L4 precursor, putative
Plasmodium knowlesi PKNH_1316000   mitochondrial ribosomal protein L4 precursor, putative
Plasmodium vivax PVX_089265   hypothetical protein, conserved
Plasmodium yoelii PY04244   hypothetical protein
Saccharomyces cerevisiae YML025C   mitochondrial 54S ribosomal protein YmL6
Schistosoma japonicum Sjp_0028620   ko:K02926 large subunit ribosomal protein L4, putative
Schistosoma mansoni Smp_124320   50S ribosomal protein L4
Schmidtea mediterranea mk4.015522.00   39S ribosomal protein L4, mitochondrial
Toxoplasma gondii TGME49_223660   50S ribosomal protein L4, putative
Treponema pallidum TP0190   50S ribosomal protein L4
Theileria parva TP01_0892   hypothetical protein, conserved
Wolbachia endosymbiont of Brugia malayi Wbm0340   50S ribosomal protein L4

Essentiality

Rv0702 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu714 this record Mycobacterium tuberculosis essential nmpdr
b3319 Escherichia coli essential goodall
CELE_T23B12.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_T23B12.2 Caenorhabditis elegans larval arrest wormbase
CELE_T23B12.2 Caenorhabditis elegans slow growth wormbase
YML025C Saccharomyces cerevisiae inviable yeastgenome
TGME49_223660 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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

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

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.

User comments

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Gene identifier Rv0702 (Mycobacterium tuberculosis), 50S ribosomal protein L4 RplD
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