Detailed view for Rv1415

Basic information

TDR Targets ID: 7004
Mycobacterium tuberculosis, Probable riboflavin biosynthesis protein RibA2 : GTP cyclohydrolase II + 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP syn
Source Database / ID:  Tuberculist 

pI: 5.564 | Length (AA): 425 | MW (Da): 46017 | 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

PF00925   GTP cyclohydrolase II
PF00926   3,4-dihydroxy-2-butanone 4-phosphate synthase

Gene Ontology

Mouse over links to read term descriptions.
GO:0008686   3,4-dihydroxy-2-butanone-4-phosphate synthase activity  
GO:0003935   GTP cyclohydrolase II activity  
GO:0009231   riboflavin biosynthetic process  

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
1 383 4i14 (A) 1 383 99.99 0 1 1.86218 -0.41
4 172 1k4i (A) 12 181 50.00 0 1 1.07625 -0.96
209 384 2bz1 (A) 3 173 55.00 0 1 1.12012 -0.86

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
  • 3MGZ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3MIO:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3MK5:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4I14:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Dormant phase, Dormant phase. hasan 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_127275)

Species Accession Gene Product
Arabidopsis thaliana AT5G64300   GTP cyclohydrolase-2
Arabidopsis thaliana AT5G59750   monofunctional riboflavin biosynthesis protein RIBA 3
Arabidopsis thaliana AT2G22450   putative riboflavin biosynthesis protein
Candida albicans CaO19.5228   Riboflavin biosynthesis, DBP synthase
Candida albicans CaO19.10380   GTP cyclohydrolase
Candida albicans CaO19.12693   3,4-dihydroxy-2-buta 4-phosphate synthase
Candida albicans CaO19.2862   GTP-cyclohydrolase 2
Chlamydia trachomatis CT_731   bifunctional GTP cyclohydratase/3,4-dihydroxy-2-butanone 4-phosphate synthase
Escherichia coli b3041   3,4-dihydroxy-2-butanone-4-phosphate synthase
Escherichia coli b1277   GTP cyclohydrolase II
Mycobacterium leprae ML0559   Probable riboflavin biosynthesis protein RibA : GTP cyclohydrolase II + 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synt
Mycobacterium tuberculosis Rv1415   Probable riboflavin biosynthesis protein RibA2 : GTP cyclohydrolase II + 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP syn
Mycobacterium ulcerans MUL_1809   bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein
Oryza sativa 4339017   Os05g0460600
Oryza sativa 4329733   Os02g0572400
Oryza sativa 9270160   Os08g0481950
Saccharomyces cerevisiae YBL033C   GTP cyclohydrolase II
Saccharomyces cerevisiae YDR487C   3,4-dihydroxy-2-butanone-4-phosphate synthase RIB3
Schmidtea mediterranea mk4.046473.02  
Wolbachia endosymbiont of Brugia malayi Wbm0312   3,4-dihydroxy-2-butanone 4-phosphate synthase
Wolbachia endosymbiont of Brugia malayi Wbm0278   GTP cyclohydrolase II

Essentiality

Rv1415 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1438 this record Mycobacterium tuberculosis essential nmpdr
b1277 Escherichia coli essential goodall
b3041 Escherichia coli non-essential goodall
YDR487C Saccharomyces cerevisiae inviable yeastgenome
Show/Hide essentiality data references
  • 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.
  • 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
  • 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.

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

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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User comments

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Gene identifier Rv1415 (Mycobacterium tuberculosis), Probable riboflavin biosynthesis protein RibA2 : GTP cyclohydrolase II + 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP syn
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