Detailed view for Rv3330

Basic information

TDR Targets ID: 5847
Mycobacterium tuberculosis, Probable penicillin-binding protein DacB1 (D-alanyl-D-alanine carboxypeptidase) (DD-peptidase) (DD-carboxypeptidase) (PBP) (DD-t
Source Database / ID:  Tuberculist 

pI: 6.2251 | Length (AA): 405 | MW (Da): 41682 | Paralog Number: 1

Signal peptide: Y | GPI Anchor: | Predicted trans-membrane segments: 1

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

PF00768   D-alanyl-D-alanine carboxypeptidase

Gene Ontology

Mouse over links to read term descriptions.
GO:0009002   serine-type D-Ala-D-Ala carboxypeptidase activity  
GO:0006508   proteolysis  

Metabolic Pathways

Peptidoglycan biosynthesis (KEGG)
Global map (KEGG)

Structural information

Modbase 3D models:

There are 2 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
59 364 4ppr (A) 59 364 99.99 0 1 1.99016 -1.63
87 404 3mzf (A) 10 346 24.00 0.000000055 1 0.970585 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:

PDB tag
  • 4P0M:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4PPR:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4RYE:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. hasan
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_129917)

Species Accession Gene Product
Escherichia coli b2010   D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 6b)
Escherichia coli b0839   D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 6a)
Escherichia coli b0632   D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5)
Mycobacterium leprae ML0691c   Probable D-alanyl-D-alanine carboxypeptidase DacB1 (PENICILLIN-BINDING PROTEIN) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) (PBP) (DD-T
Mycobacterium tuberculosis Rv3330   Probable penicillin-binding protein DacB1 (D-alanyl-D-alanine carboxypeptidase) (DD-peptidase) (DD-carboxypeptidase) (PBP) (DD-t
Mycobacterium tuberculosis Rv2911   Probable penicillin-binding protein DacB2 (D-alanyl-D-alanine carboxypeptidase) (DD-peptidase) (DD-carboxypeptidase) (PBP) (DD-t
Mycobacterium ulcerans MUL_2045   D-alanyl-D-alanine carboxypeptidase
Mycobacterium ulcerans MUL_1445   penicillin-binding protein DacC
Schmidtea mediterranea mk4.031645.03  
Schmidtea mediterranea mk4.039235.00  
Treponema pallidum TP0800   serine-type D-Ala-D-Ala carboxypeptidase (dacC)
Wolbachia endosymbiont of Brugia malayi Wbm0290   D-alanyl-D-alanine carboxypeptidase

Essentiality

Rv3330 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3390 this record Mycobacterium tuberculosis non-essential nmpdr
mtu2958 Mycobacterium tuberculosis non-essential nmpdr
b0632 Escherichia coli non-essential goodall
b0839 Escherichia coli non-essential goodall
b2010 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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
Species Known druggable target Linked compounds Reference
Staphylococcus aureus Penicillin-binding protein 4 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

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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Rv3330 (Mycobacterium tuberculosis), Probable penicillin-binding protein DacB1 (D-alanyl-D-alanine carboxypeptidase) (DD-peptidase) (DD-carboxypeptidase) (PBP) (DD-t
Title for this comment
Comment