Detailed view for Rv0009

Basic information

TDR Targets ID: 6910
Mycobacterium tuberculosis, Probable iron-regulated peptidyl-prolyl cis-trans isomerase A PpiA (PPIase A) (rotamase A)
Source Database / ID:  Tuberculist 

pI: 6.2153 | Length (AA): 182 | MW (Da): 19239 | 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

PF00160   Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD

Gene Ontology

Mouse over links to read term descriptions.
GO:0000413   protein peptidyl-prolyl isomerization  
GO:0003755   peptidyl-prolyl cis-trans isomerase activity  
GO:0006457   protein folding  

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
12 182 1w74 (A) 12 182 99.99 0 1 2.24936 -2.19
12 182 1w74 (A) 12 182 99.99 0 1 2.24936 -2.19
12 182 1w74 (A) 12 182 99.99 0 1 2.24936 -2.19

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
  • 1W74:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Lower 20-40% 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_128211)

Species Accession Gene Product
Arabidopsis thaliana AT3G44600   cyclophilin71
Babesia bovis BBOV_IV009550   peptidyl-prolyl cis-trans isomerase, putative
Brugia malayi Bm1_28740   cyclophilin-type peptidyl-prolyl cis-trans isomerase-15, Bmcyp-15
Caenorhabditis elegans CELE_Y87G2A.6   Protein CYN-15
Cryptosporidium hominis Chro.70067   protein-related
Cryptosporidium parvum cgd7_520   cyclincyclophilin like peptidyl-prolyl cis-trans isomerase fused to WD40 repeats at the N-terminus
Dictyostelium discoideum DDB_G0269054   WD40 repeat-containing protein
Drosophila melanogaster Dmel_CG3511   CG3511 gene product from transcript CG3511-RA
Escherichia coli b0525   peptidyl-prolyl cis-trans isomerase B (rotamase B)
Echinococcus granulosus EgrG_000596800   peptidylprolyl isomerase domain and WD40 repeat
Echinococcus multilocularis EmuJ_000596800   peptidylprolyl isomerase domain and WD40 repeat
Homo sapiens ENSG00000113593   peptidylprolyl isomerase domain and WD repeat containing 1
Loa Loa (eye worm) LOAG_13806   cyclophilin-type peptidyl-prolyl cis-trans isomerase-15
Loa Loa (eye worm) LOAG_09305   hypothetical protein
Mycobacterium leprae ML0011   Probable peptidyl-prolyl cis-trans isomerase PpiA (PPIase A) (Rotamase A)
Mus musculus ENSMUSG00000021713   peptidylprolyl isomerase domain and WD repeat containing 1
Mycobacterium tuberculosis Rv0009   Probable iron-regulated peptidyl-prolyl cis-trans isomerase A PpiA (PPIase A) (rotamase A)
Mycobacterium ulcerans MUL_0013   peptidyl-prolyl cis-trans isomerase A, PpiA
Neospora caninum NCLIV_009630   cyclophilin, putative
Oryza sativa 4346298   Os08g0557500
Plasmodium berghei PBANKA_1109800   peptidyl-prolyl cis-trans isomerase, putative
Plasmodium falciparum PF3D7_0510200   peptidyl-prolyl cis-trans isomerase
Plasmodium knowlesi PKNH_1023400   peptidyl-prolyl cis-trans isomerase, putative
Plasmodium vivax PVX_098070   cyclophilin, putative
Plasmodium yoelii PY03899   putative protein-related
Schistosoma japonicum Sjp_0088530   Peptidylprolyl isomerase domain and WD repeat-containing protein 1, putative
Schistosoma japonicum Sjp_0200300   ko:K01802 peptidylprolyl isomerase [EC5.2.1.8], putative
Schistosoma mansoni Smp_133820   peptidyl-prolyl cis-trans isomerase-like
Schmidtea mediterranea mk4.007066.04  
Schmidtea mediterranea mk4.007066.03  
Schmidtea mediterranea mk4.042814.00  
Schmidtea mediterranea mk4.007376.01  
Schmidtea mediterranea mk4.007376.00  
Toxoplasma gondii TGME49_320640   peptidylprolyl isomerase domain-containing protein
Treponema pallidum TP0947   peptidyl-prolyl cis-trans isomerase, cyclophilin-binding (cyp)
Theileria parva TP01_0815   cyclophilin, putative
Trichomonas vaginalis TVAG_172150   peptidyl-prolyl cis-trans isomerase, putative

Essentiality

Rv0009 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu9 this record Mycobacterium tuberculosis non-essential nmpdr
CELE_Y87G2A.6 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y87G2A.6 Caenorhabditis elegans sterile wormbase
PBANKA_1109800 Plasmodium berghei Slow plasmo
TGME49_320640 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
Species Target Length Identity Alignment span Linked Drugs Reference
Plasmodium falciparum peptidyl-prolyl cis-trans isomerase 171 aa 42.5% 146 aa Compounds References
Rattus norvegicus Cyclophilin A 164 aa 40.1% 157 aa Compounds References
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

  • Assay for FK-Binding Protein Peptidyl-Prolyl Isomerase Activity (5.2.1.8 ) 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.

User comments

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Gene identifier Rv0009 (Mycobacterium tuberculosis), Probable iron-regulated peptidyl-prolyl cis-trans isomerase A PpiA (PPIase A) (rotamase A)
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