Detailed view for Rv0286

Basic information

TDR Targets ID: 6873
Mycobacterium tuberculosis, PPE family protein PPE4

Source Database / ID: Tuberculist / Rv0286 

pI: 5.3058 | Length (AA): 513 | MW (Da): 51788 | Paralog Number: 5

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 3

Pfam domains

PF00823   PPE family

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
6 176 5xfs (B) 3 173 43.00 0 1 0.721733 0.89
6 177 4w4k (B) 3 173 30.00 0 0.75 0.560883 0.91
330 399 4x8w (H) 1 307 58.00 0 0.19 0.0148522 2.08
477 510 1nay (A) 106 139 26.00 0.21 0.01 0.402177 -1.1

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:

  • 4KXR: Structure of the Mycobacterium tuberculosis type VII secretion system chaperone EspG5 in complex with PE25-PPE41 dimer
  • Korotkova, N., Creekmore, C.C., Korotkov, K.V.
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
    2.60 X-RAY DIFFRACTION 4143 595 2013-05-27 2014-05-28 2014-10-22
  • 4W4K: Crystal structure of a PE25-PPE41 heterodimer from a type VII secretion system of M. tuberculosis
  • Ekiert, D.C., Cox, J.S.
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
    1.95 X-RAY DIFFRACTION 4069 562 2014-08-14 2014-10-01 2017-09-27
  • 4W4L: Crystal structure of EspG5 in complex with PE25 and PPE41 from the ESX-5 type VII secretion system of M. tuberculosis
  • Ekiert, D.C., Cox, J.S.
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
    2.45 X-RAY DIFFRACTION 4384 597 2014-08-14 2014-10-01 2017-09-27
  • Ligand information
  • 1,2-ETHANEDIOL C(CO)O non-polymer Search in DB
  • 5XFS: Crystal structure of PE8-PPE15 in complex with EspG5 from M. tuberculosis
  • Chen, X., Au, S.W.N.
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
    2.90 X-RAY DIFFRACTION 3853 614 2017-04-11 2017-08-30 2017-12-06

Expression

Upregulation Percent Ranking Shows this level of upregulation in
This gene ranks in the mid 40-60% group of genes. Dormant phase.
Upregulation Percent Ranking Shows this level of upregulation in
This gene ranks in the lower 0-20% group of genes. Dormant phase.
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_173655)

Species Accession Gene Product
Mycobacterium tuberculosis Rv3018c   PPE family protein PPE46
Mycobacterium tuberculosis Rv3738c   PPE family protein PPE66
Mycobacterium tuberculosis Rv3021c   PPE family protein PPE47
Mycobacterium tuberculosis Rv2123   PPE family protein PPE37
Mycobacterium tuberculosis Rv0286 this record   PPE family protein PPE4
Mycobacterium tuberculosis Rv3022c   PPE family protein PPE48
Mycobacterium ulcerans MUL_0492   PPE family protein
Mycobacterium ulcerans MUL_1154   PPE family protein
Mycobacterium ulcerans MUL_2686   PPE family protein
Mycobacterium ulcerans MUL_2932   PPE family protein
Mycobacterium ulcerans MUL_1208   PPE family protein

Essentiality

Rv0286 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu289 this record Mycobacterium tuberculosis essential nmpdr
Show/Hide essentiality data references
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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 log in using your TDR Targets username and password and send them to us using the corresponding form in this page (only visible to registered users) or contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Druggability index (range: 0 to 1): 0.1


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.

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User comments

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Gene identifier Rv0286 (Mycobacterium tuberculosis), PPE family protein PPE4
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