Detailed view for Rv1213

Basic information

TDR Targets ID: 6143
Mycobacterium tuberculosis, Glucose-1-phosphate adenylyltransferase GlgC (ADP-glucose synthase) (ADP-glucose pyrophosphorylase)
Source Database / ID:  Tuberculist 

pI: 4.9372 | Length (AA): 404 | MW (Da): 43800 | 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

PF00483   Nucleotidyl transferase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016740   transferase activity  
GO:0008878   glucose-1-phosphate adenylyltransferase activity  
GO:0016779   nucleotidyltransferase activity  
GO:0009058   biosynthetic process  
GO:0005978   glycogen 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
2 402 5l6s (N) 14 421 26.00 0 1 1.19247 0.27
8 403 3brk (X) 14 415 40.00 0 1 1.4873 -0.71
333 387 1qre (A) 129 183 13.00 0 0.45 0.388039 -1

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 20-40% 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_135249)

Species Accession Gene Product
Arabidopsis thaliana AT5G48300   glucose-1-phosphate adenylyltransferase small subunit
Chlamydia trachomatis CT_489   glucose-1-phosphate adenyltransferase
Escherichia coli b3430   glucose-1-phosphate adenylyltransferase
Mycobacterium leprae ML1069   PROBABLE GLUCOSE-1-PHOSPHATE ADENYLYLTRANSFERASE GLGC (ADP-glucose synthase) (ADP-glucose pyrophosphorylase)
Mycobacterium tuberculosis Rv1213   Glucose-1-phosphate adenylyltransferase GlgC (ADP-glucose synthase) (ADP-glucose pyrophosphorylase)
Mycobacterium ulcerans MUL_4526   glucose-1-phosphate adenylyltransferase
Oryza sativa 4346656   Os09g0298200
Oryza sativa 4345339   Os08g0345800
Trichomonas vaginalis TVAG_397470   glucose-1-phosphate thymidylyltransferase, putative

Essentiality

Rv1213 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1234 this record Mycobacterium tuberculosis non-essential nmpdr
b3430 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
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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

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

  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Mycobacterium smegmatis ( 2 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Rv1213 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Mycobacterium smegmatis ( 1 )

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 Rv1213 (Mycobacterium tuberculosis), Glucose-1-phosphate adenylyltransferase GlgC (ADP-glucose synthase) (ADP-glucose pyrophosphorylase)
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