Detailed view for Rv3464

Basic information

TDR Targets ID: 7014
Mycobacterium tuberculosis, dTDP-glucose 4,6-dehydratase RmlB
Source Database / ID:  Tuberculist 

pI: 5.3912 | Length (AA): 331 | MW (Da): 37558 | Paralog Number: 0

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

PF16363   GDP-mannose 4,6 dehydratase

Gene Ontology

Mouse over links to read term descriptions.
GO:0008460   dTDP-glucose 4,6-dehydratase activity  
GO:0050662   coenzyme binding  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0044237   cellular metabolic process  
GO:0009225   nucleotide-sugar metabolic process  
GO:0008152   metabolic process  

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
2 331 1oc2 (A) 6 345 62.00 0 1 1.83748 -1.73

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
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_127949)

Species Accession Gene Product
Arabidopsis thaliana AT3G14790   rhamnose biosynthetic enzyme 3
Arabidopsis thaliana AT1G78570   UDP-L-rhamnose synthase
Arabidopsis thaliana AT1G53500   putative NDP-L-rhamnose synthase
Brugia malayi Bm1_42170   NAD dependent epimerase/dehydratase family protein
Candida albicans CaO19.3674   dTDP glucose-6-dehydratase
Candida albicans CaO19.11158   dTDP glucose-6-dehydratase
Caenorhabditis elegans CELE_C01F1.3   Protein C01F1.3, isoform B
Caenorhabditis elegans CELE_F53B1.4   Protein F53B1.4
Dictyostelium discoideum DDB_G0279465   hypothetical protein
Escherichia coli b2041   dTDP-glucose 4,6 dehydratase, NAD(P)-binding
Escherichia coli b3788   dTDP-glucose 4,6-dehydratase
Entamoeba histolytica EHI_174070   dTDP-D-glucose 4,6-dehydratase, putative
Entamoeba histolytica EHI_125700   dTDP-D-glucose 4,6-dehydratase, putative
Homo sapiens ENSG00000088451   TDP-glucose 4,6-dehydratase
Leishmania braziliensis LbrM.26.2150   GDP-mannose 4,6 dehydratase, putative
Leishmania donovani LdBPK_262240.1   GDP-mannose 4,6 dehydratase, putative
Leishmania infantum LinJ.26.2240   GDP-mannose 4,6 dehydratase, putative
Leishmania major LmjF.26.2230   GDP-mannose 4,6 dehydratase, putative
Leishmania mexicana LmxM.26.2230   GDP-mannose 4,6 dehydratase, putative
Loa Loa (eye worm) LOAG_03637   hypothetical protein
Mycobacterium leprae ML1964   dTDP-GLUCOSE 4,6-DEHYDRATASE RMLB
Mus musculus ENSMUSG00000022130   TDP-glucose 4,6-dehydratase
Mycobacterium tuberculosis Rv3464   dTDP-glucose 4,6-dehydratase RmlB
Mycobacterium ulcerans MUL_0840   dTDP-glucose-4,6-dehydratase, RmlB
Mycobacterium ulcerans MUL_2058   hypothetical protein
Oryza sativa 4332425   Os03g0278200
Schmidtea mediterranea mk4.032167.03   dTDP-D-glucose 4,6-dehydratase
Trypanosoma cruzi TcCLB.508119.120   GDP-mannose 4,6 dehydratase, putative
Trypanosoma cruzi TcCLB.503881.20   GDP-mannose 4,6 dehydratase, putative
Trypanosoma cruzi TcCLB.507039.41   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.511019.84   GDP-mannose 4,6 dehydratase, putative
Trichomonas vaginalis TVAG_414560   DTDP-glucose 4,6-dehydratase, putative

Essentiality

Rv3464 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3525 this record Mycobacterium tuberculosis essential nmpdr
b2041 Escherichia coli non-essential goodall
b3788 Escherichia coli non-essential goodall
CELE_C01F1.3 Caenorhabditis elegans larval arrest wormbase
CELE_C01F1.3 Caenorhabditis elegans larval lethal wormbase
Show/Hide essentiality data references
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.

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): 0.7

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

2 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 Rv3464 (Mycobacterium tuberculosis), dTDP-glucose 4,6-dehydratase RmlB
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