Detailed view for Rv3316

Basic information

TDR Targets ID: 9876
Mycobacterium tuberculosis, Probable succinate dehydrogenase (cytochrome B-556 subunit) SdhC (succinic dehydrogenase) (fumarate reductase) (fumarate dehydro
Source Database / ID:  Tuberculist 

pI: 8.9788 | Length (AA): 112 | MW (Da): 12837 | Paralog Number: 0

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

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

PF01127   Succinate dehydrogenase/Fumarate reductase transmembrane subunit

Gene Ontology

Mouse over links to read term descriptions.
GO:0045281   succinate dehydrogenase complex  
GO:0016627   oxidoreductase activity, acting on the CH-CH group of donors  
GO:0016020   membrane  
GO:0009055   electron carrier activity  
GO:0000104   succinate dehydrogenase activity  
GO:0006099   tricarboxylic acid cycle  

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
1 103 2wdq (C) 24 128 23.00 0 0.08 1.06624 0.59
7 112 4ysx (C) 75 180 25.00 0.32 0.2 0.976129 1.64
48 110 1kf6 (D) 20 84 33.00 0.57 0.01 0.5892 2.38

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 80-100% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 20-40% 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_144477)

Species Accession Gene Product
Mycobacterium leprae ML0699c   Probable succinate dehydrogenase (cytochrome B-556 subunit) SdhC (SUCCINIC DEHYDROGENASE) (FUMARATE REDUCTASE) (FUMARATE DEHYDRO
Mycobacterium tuberculosis Rv3316   Probable succinate dehydrogenase (cytochrome B-556 subunit) SdhC (succinic dehydrogenase) (fumarate reductase) (fumarate dehydro
Mycobacterium ulcerans MUL_1367   succinate dehydrogenase (cytochrome B-556 subunit) SdhC

Essentiality

Rv3316 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3376 this record Mycobacterium tuberculosis non-essential nmpdr
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.

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
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

  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Mycobacterium phlei ( 1 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Rv3316 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Mycobacterium phlei ( 1 )

Bibliographic References

69 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.

User comments

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Gene identifier Rv3316 (Mycobacterium tuberculosis), Probable succinate dehydrogenase (cytochrome B-556 subunit) SdhC (succinic dehydrogenase) (fumarate reductase) (fumarate dehydro
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