Detailed view for Rv2280

Basic information

TDR Targets ID: 8453
Mycobacterium tuberculosis, Probable dehydrogenase
Source Database / ID:  Tuberculist 

pI: 4.6372 | Length (AA): 459 | MW (Da): 48052 | 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

PF01565   FAD binding domain
PF02913   FAD linked oxidases, C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016614   oxidoreductase activity, acting on CH-OH group of donors  
GO:0050660   FAD binding  
GO:0016491   oxidoreductase activity  
GO:0008762   UDP-N-acetylmuramate dehydrogenase activity  
GO:0003824   catalytic activity  
GO:0055114   oxidation reduction  

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
1 456 1e8g (A) 21 547 23.00 0 1 1.08926 0.48
2 455 3pm9 (A) 14 474 30.00 0 1 1.33191 -0.11
3 455 3pm9 (A) 15 474 34.00 0 1 1.31603 0.24
13 94 5awv (A) 31 112 13.00 0 0.1 0.374449 -0.82

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_127093)

Species Accession Gene Product
Arabidopsis thaliana AT5G06580   D-lactate dehydrogenase [cytochrome]
Brugia malayi Bm1_34710   FAD linked oxidases, C-terminal domain containing protein
Candida albicans CaO19.5805   lactate cytochrome c oxidoreductase
Candida albicans CaO19.13227   lactate cytochrome c oxidoreductase
Candida albicans CaO19.13464   D-lactate dehydrogenase (cytochrome)
Candida albicans CaO19.14047   Mitochondrial lactate ferricytochrome c oxidoreductase
Candida albicans CaO19.6043   D-lactate dehydrogenase (cytochrome)
Candida albicans CaO19.6755   Mitochondrial lactate ferricytochrome c oxidoreductase
Caenorhabditis elegans CELE_F32D8.12   Protein F32D8.12, isoform C
Dictyostelium discoideum DDB_G0270806   hypothetical protein
Escherichia coli b1687   putative FAD-linked oxidoreductase
Escherichia coli b2979   glycolate oxidase subunit, FAD-linked
Homo sapiens ENSG00000166816   lactate dehydrogenase D
Leishmania braziliensis LbrM.27.2200   D-lactate dehydrogenase-like protein
Leishmania donovani LdBPK_290290.1   D-lactate dehydrogenase-like protein
Leishmania donovani LdBPK_271940.1   D-lactate dehydrogenase-like protein
Leishmania infantum LinJ.27.1940   D-lactate dehydrogenase-like protein
Leishmania infantum LinJ.29.0290   D-lactate dehydrogenase-like protein
Leishmania major LmjF.29.0280   D-lactate dehydrogenase-like protein
Leishmania major LmjF.27.2020   D-lactate dehydrogenase-like protein
Leishmania mexicana LmxM.08_29.0280  
Leishmania mexicana LmxM.27.2020   D-lactate dehydrogenase-like protein
Loa Loa (eye worm) LOAG_02950   hypothetical protein
Mycobacterium leprae ML1103c   PROBABLE OXIDOREDUCTASE
Mus musculus ENSMUSG00000031958   lactate dehydrogenase D
Mycobacterium tuberculosis Rv2280   Probable dehydrogenase
Mycobacterium tuberculosis Rv1257c   Probable oxidoreductase
Mycobacterium ulcerans MUL_4485   oxidoreductase
Oryza sativa 9270233   Os07g0163000
Saccharomyces cerevisiae YDL174C   Dld1p

Essentiality

Rv2280 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2315 this record Mycobacterium tuberculosis non-essential nmpdr
b1687 Escherichia coli non-essential goodall
b2979 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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

Druggability index (range: 0 to 1): 0.3

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.

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 Rv2280 (Mycobacterium tuberculosis), Probable dehydrogenase
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