Detailed view for Rv3319

Basic information

TDR Targets ID: 9875
Mycobacterium tuberculosis, Probable succinate dehydrogenase (iron-sulphur protein subunit) SdhB (succinic dehydrogenase) (fumarate reductase) (fumarate deh
Source Database / ID:  Tuberculist 

pI: 7.4017 | Length (AA): 263 | MW (Da): 29335 | Paralog Number: 1

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG2

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

PF13085   2Fe-2S iron-sulfur cluster binding domain
PF13183   4Fe-4S dicluster domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0009055   electron carrier activity  
GO:0051536   iron-sulfur cluster binding  
GO:0006099   tricarboxylic acid cycle  
GO:0055114   oxidation reduction  

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
21 263 2h88 (B) 9 246 28.00 0 1 1.21665 0.4
24 260 1kf6 (B) 6 232 38.00 0 1 1.36024 -0.46
28 260 2wdq (B) 7 234 46.00 0 1 1.37503 -0.15

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 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_126893)

Species Accession Gene Product
Arabidopsis thaliana AT5G40650   succinate dehydrogenase [ubiquinone] iron-sulfur subunit 2
Arabidopsis thaliana AT5G65165   succinate dehydrogenase [ubiquinone] iron-sulfur subunit 3
Arabidopsis thaliana AT3G27380   succinate dehydrogenase [ubiquinone] iron-sulfur subunit 1
Babesia bovis BBOV_IV005280   succinate dehydrogenase iron-sulfur subunit, putative
Brugia malayi Bm1_17690   succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial
Candida albicans CaO19.8251   iron-sulfur subunit of succinate dehydrogenase
Candida albicans CaO19.637   iron-sulfur subunit of succinate dehydrogenase
Caenorhabditis elegans CELE_F42A8.2   Protein SDHB-1
Chlamydia trachomatis CT_591   succinate dehydrogenase iron sulfur subunit
Dictyostelium discoideum DDB_G0270120   complex II, iron-sulfur protein subunit
Drosophila melanogaster Dmel_CG7349   CG7349 gene product from transcript CG7349-RC
Drosophila melanogaster Dmel_CG3283   Succinate dehydrogenase B
Escherichia coli b4153   fumarate reductase (anaerobic), Fe-S subunit
Escherichia coli b0724   succinate dehydrogenase, FeS subunit
Echinococcus granulosus EgrG_000416100   succinate dehydrogenase (ubiquinone) iron sulfur
Echinococcus granulosus EgrG_000416200   succinate dehydrogenase ubiquinone iron sulfur
Echinococcus multilocularis EmuJ_000416100   succinate dehydrogenase iron sulfur protein
Echinococcus multilocularis EmuJ_000416200   succinate dehydrogenase (ubiquinone) iron sulfur
Echinococcus multilocularis EmuJ_000416000   succinate dehydrogenase (ubiquinone) iron sulfur
Homo sapiens ENSG00000117118   succinate dehydrogenase complex, subunit B, iron sulfur (Ip)
Leishmania braziliensis LbrM.15.1030   succinate dehydrogenase, putative
Leishmania braziliensis LbrM.23.1530   hypothetical protein, conserved
Leishmania donovani LdBPK_151050.1   succinate dehydrogenase, putative
Leishmania donovani LdBPK_231680.1   succinate dehydrogenase and fumarate reductase iron-sulfur protein, putative
Leishmania infantum LinJ.23.1680   hypothetical protein, conserved
Leishmania infantum LinJ.15.1050   succinate dehydrogenase, putative
Leishmania major LmjF.23.1410   hypothetical protein, conserved
Leishmania major LmjF.15.0990   succinate dehydrogenase, putative
Leishmania mexicana LmxM.15.0990   succinate dehydrogenase, putative
Leishmania mexicana LmxM.23.1410   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_10155   succinate dehydrogenase iron-sulfur protein
Mycobacterium leprae ML0696c   Probable succinate dehydrogenase (iron-sulfur protein subunit) SdhB (SUCCINIC DEHYDROGENASE) (FUMARATE REDUCTASE) (FUMARATE DEHY
Mus musculus ENSMUSG00000009863   succinate dehydrogenase complex, subunit B, iron sulfur (Ip)
Mycobacterium tuberculosis Rv3319   Probable succinate dehydrogenase (iron-sulphur protein subunit) SdhB (succinic dehydrogenase) (fumarate reductase) (fumarate deh
Mycobacterium tuberculosis Rv1553   Probable fumarate reductase [iron-sulfur subunit] FrdB (fumarate dehydrogenase) (fumaric hydrogenase)
Mycobacterium ulcerans MUL_1370   succinate dehydrogenase iron-sulfur subunit
Neospora caninum NCLIV_052230   Succinate dehydrogenase iron-sulfur subunit, related
Oryza sativa 4346890   Os09g0370300
Oryza sativa 4344541   Os08g0120000
Plasmodium berghei PBANKA_1428800   iron-sulfur subunit of succinate dehydrogenase, putative
Plasmodium falciparum PF3D7_1212800   iron-sulfur subunit of succinate dehydrogenase
Plasmodium knowlesi PKNH_1432200   iron-sulfur subunit of succinate dehydrogenase, putative
Plasmodium vivax PVX_123345   iron-sulfur subunit of succinate dehydrogenase, putative
Plasmodium yoelii PY04921   succinate dehydrogenase iron-sulfur subunit
Saccharomyces cerevisiae YLL041C   succinate dehydrogenase iron-sulfur protein subunit SDH2
Schistosoma japonicum Sjp_0062650   ko:K00235 succinate dehydrogenase (ubiquinone) iron-sulfur protein precursor, putative
Schistosoma mansoni Smp_089640.2   succinate dehydrogenase iron-sulfur protein
Schistosoma mansoni Smp_089640.3   succinate dehydrogenase iron-sulfur protein
Schmidtea mediterranea mk4.000382.04   Putative succinate dehydrogenase iron-sulfur protein
Trypanosoma brucei gambiense Tbg972.8.3140   electron transfer protein, putative
Trypanosoma brucei gambiense Tbg972.9.3110   succinate dehydrogenase, putative
Trypanosoma brucei Tb927.8.3380   succinate dehydrogenase iron-sulfur subunit
Trypanosoma brucei Tb927.9.5960   succinate dehydrogenase iron-sulfur subunit, putative
Trypanosoma congolense TcIL3000_8_3420   electron transfer protein, putative
Trypanosoma congolense TcIL3000_9_2010   succinate dehydrogenase, putative
Trypanosoma cruzi TcCLB.505843.24   succinate dehydrogenase, putative
Trypanosoma cruzi TcCLB.504949.30   succinate dehydrogenase iron-sulfur subunit
Trypanosoma cruzi TcCLB.509769.60   succinate dehydrogenase iron-sulfur subunit
Toxoplasma gondii TGME49_215280   succinate dehydrogenase [ubiquinone] iron-sulfur protein
Theileria parva TP01_0210   succinate dehydrogenase iron-sulfur subunit, putative
Wolbachia endosymbiont of Brugia malayi Wbm0600   succinate dehydrogenase iron-sulfur subunit

Essentiality

Rv3319 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1581 Mycobacterium tuberculosis non-essential nmpdr
mtu3379 this record Mycobacterium tuberculosis non-essential nmpdr
Tb09.160.4380 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.160.4380 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb09.160.4380 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.160.4380 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.8.3380 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.8.3380 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.8.3380 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.8.3380 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b0724 Escherichia coli non-essential goodall
b4153 Escherichia coli non-essential goodall
CELE_F42A8.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_F42A8.2 Caenorhabditis elegans larval arrest wormbase
CELE_F42A8.2 Caenorhabditis elegans slow growth wormbase
CELE_F42A8.2 Caenorhabditis elegans sterile wormbase
PBANKA_1428800 Plasmodium berghei Dispensable plasmo
TGME49_215280 Toxoplasma gondii Probably essential sidik
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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
Species Known druggable target Linked compounds Reference
Plasmodium falciparum iron-sulfur subunit of succinate dehydrogenase Compounds References
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
    Rv3319 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.

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Gene identifier Rv3319 (Mycobacterium tuberculosis), Probable succinate dehydrogenase (iron-sulphur protein subunit) SdhB (succinic dehydrogenase) (fumarate reductase) (fumarate deh
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