Detailed view for Rv1380

Basic information

TDR Targets ID: 6971
Mycobacterium tuberculosis, Probable aspartate carbamoyltransferase PyrB (ATCase) (aspartate transcarbamylase)
Source Database / ID:  Tuberculist 

pI: 7.088 | Length (AA): 319 | MW (Da): 33819 | Paralog Number: 0

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

PF00185   Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
PF02729   Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016743   carboxyl- or carbamoyltransferase activity  
GO:0016597   amino acid binding  
GO:0004070   aspartate carbamoyltransferase activity  
GO:0006520   amino acid metabolic process  
GO:0006207   'de novo' pyrimidine base biosynthetic process  

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
1 313 3q98 (A) 19 382 19.00 0 1 0.992691 0.21
4 307 3r7f (A) 2 289 39.00 0 1 1.45908 -0.74
4 307 5g1n (A) 1924 2222 39.00 0 1 1.40008 -0.45
4 307 1ml4 (A) 6 305 36.00 0 1 1.39608 -0.71

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 0-20% 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_128535)

Species Accession Gene Product
Arabidopsis thaliana AT3G20330   aspartate carbamoyltransferase
Babesia bovis BBOV_I003660   aspartate transcarbamoylase, putative
Escherichia coli b4245   aspartate carbamoyltransferase, catalytic subunit
Leishmania braziliensis LbrM.16.0560   aspartate carbamoyltransferase, putative
Leishmania donovani LdBPK_160550.1   aspartate carbamoyltransferase, putative
Leishmania infantum LinJ.16.0550   aspartate carbamoyltransferase, putative
Leishmania major LmjF.16.0540   aspartate carbamoyltransferase, putative
Leishmania mexicana LmxM.16.0540   aspartate carbamoyltransferase, putative
Mycobacterium leprae ML0532   Probable aspartate carbamoyltransferase PyrB (Aspartate transcarbamylase) (ATCase)
Mycobacterium tuberculosis Rv1380   Probable aspartate carbamoyltransferase PyrB (ATCase) (aspartate transcarbamylase)
Mycobacterium ulcerans MUL_1780   aspartate carbamoyltransferase catalytic subunit
Neospora caninum NCLIV_043140   aspartate carbamoyltransferase, putative
Oryza sativa 4345071   Os08g0248800
Plasmodium berghei PBANKA_1357700   aspartate carbamoyltransferase, putative
Plasmodium falciparum PF3D7_1344800   aspartate carbamoyltransferase
Plasmodium knowlesi PKNH_1256500   aspartate carbamoyltransferase, putative
Plasmodium vivax PVX_083135   aspartate carbamoyltransferase, putative
Plasmodium yoelii PY06210   aspartate carbamoyltransferase
Trypanosoma brucei gambiense Tbg972.5.5310   aspartate carbamoyltransferase, putative
Trypanosoma brucei Tb927.5.3820   aspartate carbamoyltransferase, putative
Trypanosoma congolense TcIL3000_5_4290   aspartate carbamoyltransferase, putative
Trypanosoma cruzi TcCLB.511643.30   aspartate carbamoyltransferase, putative
Trypanosoma cruzi TcCLB.508375.30   aspartate carbamoyltransferase, putative
Trypanosoma cruzi TcCLB.511923.110   aspartate carbamoyltransferase, putative
Trypanosoma cruzi TcCLB.507091.50   aspartate carbamoyltransferase, putative
Toxoplasma gondii TGME49_291640   aspartate carbamoyltransferase
Theileria parva TP01_0476   aspartate carbamoyltransferase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0385   aspartate carbamoyltransferase

Essentiality

Rv1380 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1403 this record Mycobacterium tuberculosis essential nmpdr
Tb927.5.3820 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.5.3820 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.5.3820 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.5.3820 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b4245 Escherichia coli non-essential goodall
PBANKA_1357700 Plasmodium berghei Essential plasmo
TGME49_291640 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.

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

  • Assay for Aspartate Transcarbamylase (2.1.3.2 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

4 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 Rv1380 (Mycobacterium tuberculosis), Probable aspartate carbamoyltransferase PyrB (ATCase) (aspartate transcarbamylase)
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