Detailed view for Rv3417c

Basic information

TDR Targets ID: 6184
Mycobacterium tuberculosis, 60 kDa chaperonin 1 GroEL1 (protein CPN60-1) (GroEL protein 1)
Source Database / ID:  Tuberculist 

pI: 4.7422 | Length (AA): 539 | MW (Da): 55877 | 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

PF00118   TCP-1/cpn60 chaperonin family

Gene Ontology

Mouse over links to read term descriptions.
GO:0042026   protein refolding  
GO:0005737   cytoplasm  
GO:0005524   ATP binding  
GO:0005515   protein binding  
GO:0044267   cellular protein metabolic process  
GO:0006457   protein folding  

Metabolic Pathways

RNA degradation (KEGG)
Tuberculosis (KEGG)

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
2 526 1kp8 (A) 3 526 52.00 0.000000012 1 1.60423 -0.52
184 377 3m6c (A) 184 377 99.99 0 1 1.61213 -1.6
190 333 1srv (A) 192 335 58.00 0 1 1.11636 -1.77

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
  • 1SJP:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3M6C:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3RTK:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Mid 40-60% 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_127343)

Species Accession Gene Product
Arabidopsis thaliana AT1G24510   T-complex protein 1 subunit epsilon
Babesia bovis BBOV_II004650   T-complex protein 1 epsilon subunit, putative
Brugia malayi Bm1_47485   T-complex protein 1, epsilon subunit
Candida albicans CaO19.9828   similar to S. cerevisiae CCT5 (YJR064W) subunit of chaperonin Cct ring complex involved in cytoskeleton assembly and protein fol
Candida albicans CaO19.2288   similar to S. cerevisiae CCT5 (YJR064W) subunit of chaperonin Cct ring complex involved in cytoskeleton assembly and protein fol
Caenorhabditis elegans CELE_C07G2.3   Protein CCT-5, isoform B
Cryptosporidium hominis Chro.70357   CCTepsilon subunit
Cryptosporidium parvum cgd7_3180   T complex chaperonin
Dictyostelium discoideum DDB_G0281849   chaperonin containing TCP1 epsilon subunit
Drosophila melanogaster Dmel_CG8439   T-complex Chaperonin 5
Echinococcus granulosus EgrG_000717700   chaperonin containing TCP1 subunit 5 epsilon
Entamoeba histolytica EHI_155450   chaperonin containing TCP-1 epsilon subunit, putative
Echinococcus multilocularis EmuJ_000717700   chaperonin containing TCP1, subunit 5 (epsilon)
Giardia lamblia GL50803_11992   TCP-1 chaperonin subunit epsilon
Homo sapiens ENSG00000150753   chaperonin containing TCP1, subunit 5 (epsilon)
Leishmania braziliensis LbrM.32.1100   chaperonin containing t-complex protein, putative
Leishmania donovani LdBPK_321060.1   chaperonin containing t-complex protein, putative
Leishmania infantum LinJ.32.1060   chaperonin containing t-complex protein, putative
Leishmania major LmjF.32.1000   chaperonin containing t-complex protein, putative
Leishmania mexicana LmxM.31.1000   chaperonin containing t-complex protein, putative
Loa Loa (eye worm) LOAG_06719   CCT-5 protein
Mycobacterium leprae ML0381   60 kDa chaperonin 1 GroEL1 (Protein Cpn60-1) (groEL protein 1)
Mus musculus ENSMUSG00000022234   chaperonin containing Tcp1, subunit 5 (epsilon)
Mycobacterium tuberculosis Rv3417c   60 kDa chaperonin 1 GroEL1 (protein CPN60-1) (GroEL protein 1)
Mycobacterium ulcerans MUL_0886   chaperonin GroEL
Neospora caninum NCLIV_022560   Thermosome subunit, related
Oryza sativa 4341310   Os06g0562600
Plasmodium berghei PBANKA_1218200   T-complex protein 1 subunit epsilon, putative
Plasmodium falciparum PF3D7_0320300   T-complex protein 1 subunit epsilon
Plasmodium knowlesi PKNH_0820900   T-complex protein 1 subunit epsilon, putative
Plasmodium vivax PVX_095220   T-complex protein 1 subunit epsilon, putative
Plasmodium yoelii PY00598   T-complex protein 1 epsilon subunit
Saccharomyces cerevisiae YJR064W   Cct5p
Schistosoma japonicum Sjp_0208180   ko:K09497 T-complex protein 1 subunit epsilon, putative
Schistosoma mansoni Smp_063420   chaperonin containing t-complex protein 1 epsilon subunit tcpe
Schmidtea mediterranea mk4.002150.02   T-complex protein 1 subunit epsilon
Trypanosoma brucei gambiense Tbg972.11.15960   T-complex protein 1, epsilon subunit, putative
Trypanosoma brucei Tb927.11.14250   T-complex protein 1, epsilon subunit, putative
Trypanosoma congolense TcIL3000.11.14560   T-complex protein 1, epsilon subunit, putative
Trypanosoma cruzi TcCLB.511725.250   chaperonin containing t-complex protein, putative
Toxoplasma gondii TGME49_202370   T-complex protein 1, epsilon subunit (TCP-1-epsilon), putative
Theileria parva TP02_0289   T-complex protein 1, epsilon subunit, putative
Trichomonas vaginalis TVAG_147070   chaperonin containing t-complex protein 1, delta subunit, tcpd, putative
Trichomonas vaginalis TVAG_272330   chaperonin containing t-complex protein 1, delta subunit, tcpd, putative

Essentiality

Rv3417c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
this record Mycobacterium tuberculosis essential nmpdr
Tb11.01.5860 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.5860 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.5860 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.5860 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C07G2.3 Caenorhabditis elegans adult lethal wormbase
CELE_C07G2.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_C07G2.3 Caenorhabditis elegans larval arrest wormbase
CELE_C07G2.3 Caenorhabditis elegans sterile wormbase
YJR064W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1218200 Plasmodium berghei Essential plasmo
TGME49_202370 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • 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.
  • 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

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): 0.2

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 Rv3417c (Mycobacterium tuberculosis), 60 kDa chaperonin 1 GroEL1 (protein CPN60-1) (GroEL protein 1)
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