Detailed view for Rv0432

Basic information

TDR Targets ID: 9912
Mycobacterium tuberculosis, Periplasmic superoxide dismutase [Cu-Zn] SodC
Source Database / ID:  Tuberculist 

pI: 6.4148 | Length (AA): 240 | MW (Da): 23844 | Paralog Number: 0

Signal peptide: Y | 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

PF00080   Copper/zinc superoxide dismutase (SODC)

Gene Ontology

Mouse over links to read term descriptions.
GO:0046872   metal ion binding  
GO:0004784   superoxide dismutase activity  
GO:0055114   oxidation reduction  
GO:0006801   superoxide metabolic process  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
70 240 1pzs (A) 1 171 99.99 0 1 1.9366 -1.35

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:

PDB tag
  • 1PZS:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

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
  • 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_127584)

Species Accession Gene Product
Arabidopsis thaliana AT2G28190   copper/zinc superoxide dismutase 2
Arabidopsis thaliana AT5G18100   copper/zinc superoxide dismutase 3
Arabidopsis thaliana AT1G08830   superoxide dismutase [Cu-Zn]
Caenorhabditis elegans CELE_F55H2.1   Protein SOD-4, isoform A
Caenorhabditis elegans CELE_C15F1.7   Protein SOD-1, isoform B
Caenorhabditis elegans CELE_ZK430.3   Protein SOD-5
Dictyostelium discoideum DDB_G0290343   superoxide dismutase
Dictyostelium discoideum DDB_G0281461   superoxide dismutase
Dictyostelium discoideum DDB_G0267420   superoxide dismutase
Dictyostelium discoideum DDB_G0281493   superoxide dismutase
Drosophila melanogaster Dmel_CG9027   Superoxide dismutase 3
Drosophila melanogaster Dmel_CG11793   Superoxide dismutase
Escherichia coli b1646   superoxide dismutase, Cu, Zn, periplasmic
Echinococcus granulosus EgrG_000638300   superoxide dismutase 1 soluble
Echinococcus multilocularis EmuJ_000638300   superoxide dismutase 1, soluble
Homo sapiens ENSG00000142168   superoxide dismutase 1, soluble
Loa Loa (eye worm) LOAG_13115   extracellular Cu/Zn superoxide dismutase
Loa Loa (eye worm) LOAG_15070   Cu/Zn superoxide dismutase 2
Loa Loa (eye worm) LOAG_13117   superoxide dismutase
Mycobacterium leprae ML1925c   PROBABLE PERIPLASMIC SUPEROXIDE DISMUTASE [CU-ZN] SODC
Mus musculus ENSMUSG00000022982   superoxide dismutase 1, soluble
Mycobacterium tuberculosis Rv0432   Periplasmic superoxide dismutase [Cu-Zn] SodC
Mycobacterium ulcerans MUL_1379   periplasmic superoxide dismutase [Cu-Zn] SodC
Oryza sativa 4332846   Os03g0351500
Oryza sativa 4344210   Os07g0665200
Oryza sativa 4332082   Os03g0219200
Oryza sativa 4346329   Os08g0561700
Saccharomyces cerevisiae YJR104C   superoxide dismutase SOD1
Schistosoma japonicum Sjp_0202510   ko:K04565 Cu/Zn superoxide dismutase [EC1.15.1.1C], putative
Schistosoma mansoni Smp_176200.1   hypothetical protein
Schistosoma mansoni Smp_176200.2   superoxide dismutase [Cu-Zn]
Schmidtea mediterranea mk4.001372.12   Extracellular superoxide dismutase
Schmidtea mediterranea mk4.002589.08   Extracellular superoxide dismutase
Schmidtea mediterranea mk4.037492.01  
Schmidtea mediterranea mk4.005126.00   Extracellular superoxide dismutase

Essentiality

Rv0432 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu435 this record Mycobacterium tuberculosis non-essential nmpdr
b1646 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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

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

  • Assay for Superoxide Dismutase (1.15.1.1 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.
  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Mycobacterium phlei ( 1 )

Reagent availability

No reagent availability information for this target.

Bibliographic References

142 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 Rv0432 (Mycobacterium tuberculosis), Periplasmic superoxide dismutase [Cu-Zn] SodC
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