Detailed view for LbrM.15.1230

Basic information

TDR Targets ID: 428717
Leishmania braziliensis, mitochondrial DNA topoisomerase II
Source Database / ID: 

pI: 9.866 | Length (AA): 1239 | MW (Da): 139189 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG

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

PF00204   DNA gyrase B
PF00521   DNA gyrase/topoisomerase IV, subunit A
PF01751   Toprim domain
PF02518   Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
PF16898   C-terminal associated domain of TOPRIM

Gene Ontology

Mouse over links to read term descriptions.
GO:0003918   DNA topoisomerase (ATP-hydrolyzing) activity  
GO:0005524   ATP binding  
GO:0003677   DNA binding  
GO:0006265   DNA topological change  
GO:0006259   DNA metabolic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 6 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 1s16 (A) 1005 1383 20.00 0 1 0.527848 -0.23
4 1118 4gfh (A) 9 1176 31.00 0 1 1.24612 0.05
414 1123 4fm9 (A) 435 1190 37.00 0 1 0.913743 0.13
419 584 5iwi (B) 417 607 27.00 0 1 0.531379 -1.17
682 1239 1zvu (A) 28 594 19.00 0 1 0.530563 1.01
1024 1231 4tql (A) 9 223 11.00 0.067 0.01 0.264077 -0.14

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_128755)

Species Accession Gene Product
Arabidopsis thaliana AT3G10270   DNA gyrase subunit B
Arabidopsis thaliana AT5G04130   DNA gyrase subunit B
Babesia bovis BBOV_IV011850   DNA gyrase subunit B, putative
Chlamydia trachomatis CT_190   DNA gyrase subunit B
Escherichia coli b3699   DNA gyrase, subunit B
Leishmania braziliensis LbrM.15.1230   mitochondrial DNA topoisomerase II
Leishmania donovani LdBPK_151310.1   mitochondrial DNA topoisomerase II
Leishmania infantum LinJ.15.1310   mitochondrial DNA topoisomerase II
Leishmania major LmjF.15.1290   mitochondrial DNA topoisomerase II
Leishmania mexicana LmxM.15.1290   mitochondrial DNA topoisomerase II
Mycobacterium leprae ML0005   Probable DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (Type II DNA topoisomerase)
Mycobacterium tuberculosis Rv0005   DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase)
Mycobacterium ulcerans MUL_0005   DNA gyrase subunit B
Neospora caninum NCLIV_006680   hypothetical protein
Oryza sativa 4326261   Os01g0268300
Plasmodium berghei PBANKA_1454000   DNA gyrase subunit B, putative
Plasmodium falciparum PF3D7_1239500   DNA gyrase subunit B
Plasmodium knowlesi PKNH_1459600   DNA gyrase subunit B, putative
Plasmodium vivax PVX_100925   DNA gyrase subunit B, putative
Plasmodium yoelii PY04024   DNA topoisomerase II, putative
Trypanosoma brucei gambiense Tbg972.9.2960   DNA topoisomerase II, putative
Trypanosoma brucei Tb927.9.5590   DNA topoisomerase ii
Trypanosoma congolense TcIL3000_0_04850   DNA topoisomerase II, putative
Trypanosoma cruzi TcCLB.506445.60   mitochondrial DNA topoisomerase II, putative
Trypanosoma cruzi TcCLB.508277.370   mitochondrial DNA topoisomerase II, putative
Toxoplasma gondii TGME49_297780   ATPase/histidine kinase/DNA gyrase B/HSP90 domain-containing protein
Treponema pallidum TP1006   DNA gyrase, subunit B (gyrB)
Theileria parva TP01_1125   DNA gyrase subunit B, putative
Wolbachia endosymbiont of Brugia malayi Wbm0764   DNA gyrase, topoisomerase II, B subunit, GyrB

Essentiality

LbrM.15.1230 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu5 Mycobacterium tuberculosis essential nmpdr
Tb09.160.4090 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.160.4090 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.160.4090 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.160.4090 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3699 Escherichia coli essential goodall
PBANKA_1454000 Plasmodium berghei Essential plasmo
TGME49_297780 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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
Species Known druggable target Linked compounds Reference
Staphylococcus aureus subsp. aureus Mu50 DNA gyrase Compounds References
Streptococcus pneumoniae ParE Compounds References
Trypanosoma cruzi mitochondrial DNA topoisomerase II, putative Compounds References
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) DNA gyrase subunit B Compounds References
Leishmania major mitochondrial DNA topoisomerase II Compounds References
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) DNA gyrase subunit B Compounds References
Mycobacterium tuberculosis DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase) Compounds References
Mycobacterium smegmatis DNA gyrase subunit B Compounds References
Staphylococcus aureus DNA gyrase subunit B Compounds References
Plasmodium falciparum DNA gyrase subunit B Compounds References
Staphylococcus aureus DNA topoisomerase 4 subunit B Compounds References
Escherichia coli DNA gyrase, subunit B Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Staphylococcus aureus DNA gyrase 644 aa 23.8% 622 aa Compounds References
Staphylococcus aureus Topoisomerase IV 663 aa 25.0% 621 aa Compounds References
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

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Gene identifier LbrM.15.1230 (Leishmania braziliensis), mitochondrial DNA topoisomerase II
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