Detailed view for Rv3553

Basic information

TDR Targets ID: 9185
Mycobacterium tuberculosis, Possible oxidoreductase
Source Database / ID:  Tuberculist 

pI: 9.8518 | Length (AA): 355 | MW (Da): 36831 | Paralog Number: 1

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

PF03060   Nitronate monooxygenase

Gene Ontology

Mouse over links to read term descriptions.
GO:0018580   2-nitropropane dioxygenase activity  
GO:0003824   catalytic activity  
GO:0055114   oxidation reduction  
GO:0008152   metabolic process  

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
3 249 4xwu (A) 57 494 26.00 0.013 1 0.950275 -0.27
3 354 5gvh (A) 3 312 38.00 0 1 1.27225 0.32
3 348 2gjl (A) 4 318 35.00 0 1 1.24135 0.06
4 354 5gvj (A) 4 312 40.00 0.00052 1 1.22553 0.43

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 60-80% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Mid 40-60% 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_129399)

Species Accession Gene Product
Arabidopsis thaliana AT5G64250   Aldolase-type TIM barrel family protein
Candida albicans CaO19.7204   potential fungal 2-nitropropane dioxygenase similar to S. cerevisiae YJR149W
Candida albicans CaO19_7204   hypothetical protein
Dictyostelium discoideum DDB_G0275593   hypothetical protein
Leishmania braziliensis LbrM.20.0540   enoyl-[acyl-carrier-protein] reductase, putative
Leishmania braziliensis LbrM.21.1500   2-nitropropane dioxygenase, putative
Leishmania donovani LdBPK_340630.1   enoyl-[acyl-carrier-protein] reductase, putative
Leishmania infantum LinJ.34.0630   enoyl-[acyl-carrier-protein] reductase, putative
Leishmania major LmjF.34.0610   enoyl-[acyl-carrier-protein] reductase, putative
Leishmania mexicana LmxM.33.0610   enoyl-[acyl-carrier-protein] reductase, putative
Mycobacterium tuberculosis Rv2781c   Possible alanine rich oxidoreductase
Mycobacterium tuberculosis Rv3553   Possible oxidoreductase
Mycobacterium ulcerans MUL_4116   2-nitropropane dioxygenase
Mycobacterium ulcerans MUL_2153   hypothetical protein
Oryza sativa 4345877   Os08g0485400
Saccharomyces cerevisiae YJR149W   hypothetical protein
Trichomonas vaginalis TVAG_479680   2-nitropropane dioxygenase precursor, putative
Wolbachia endosymbiont of Brugia malayi Wbm0753   trans-2-enoyl-ACP reductase, FabK

Essentiality

Rv3553 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2828 Mycobacterium tuberculosis non-essential nmpdr
mtu3614 this record Mycobacterium tuberculosis non-essential nmpdr
Show/Hide essentiality data references
  • 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.
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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

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
Species Known druggable target Linked compounds Reference
Streptococcus pneumoniae Enoyl-(Acyl-carrier-protein) reductase Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0397 1 1
0.0157 1 0.5
0.0157 1 1
0.0526 0.3609 1
0.0157 1 1
0.0683 1 1
0.0988 1 1
0.0534 0.6004 1
0.0401 1 1
0.0395 1 1
0.0454 0.6178 1
0.0157 1 1
0.0157 0.3225 1
0.0578 1 1
0.0426 1 1
0.0157 1 1
0.0534 0.6004 1
0.0278 1 1
0.0157 1 1
0.0688 1 1
0.0411 1 1
0.1111 1 1
0.069 1 0.5
0.0988 1 1
0.0534 0.6004 1
0.0157 0.5 0.5
0.1111 1 1
0.0557 1 1
0.0157 1 1
0.0157 1 1
0.0534 0.6004 1
0.0987 1 1
0.0157 1 1
0.0827 1 1
0.0424 1 1
0.0534 0.6004 1
0.0862 1 1
0.0157 1 1
0.0157 1 1
0.0284 0.7402 1
0.0987 1 1

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.

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Gene identifier Rv3553 (Mycobacterium tuberculosis), Possible oxidoreductase
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