Detailed view for Rv0005

Basic information

TDR Targets ID: 6194
Mycobacterium tuberculosis, DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase)

Source Database / ID: Tuberculist / Rv0005 

pI: 6.342 | Length (AA): 675 | MW (Da): 74059 | Paralog Number: 0

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

Pfam domains

PF00204   DNA gyrase B
PF00986   DNA gyrase B subunit, carboxyl terminus
PF01751   Toprim domain
PF02518   Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase

Gene Ontology

Mouse over links to read term descriptions.
GO:0003918   DNA topoisomerase (ATP-hydrolyzing) activity  
GO:0005694   chromosome  
GO:0005524   ATP binding  
GO:0003677   DNA binding  
GO:0006265   DNA topological change  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 12 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
49 463 3zkb (B) 10 424 99.99 0 1 1.66833 -0.84
64 708 4i3h (A) 24 639 48.00 0 1 1.21576 0.71
465 714 5bs8 (B) 426 675 99.99 0 1 1.50124 -0.88
480 621 5npk (B) 417 592 62.00 0 1 1.02408 -1.41
49 463 3zkb (B) 10 424 99.99 0 1 1.66833 -0.84
64 708 4i3h (A) 24 639 48.00 0 1 1.21576 0.71
465 714 5bs8 (B) 426 675 99.99 0 1 1.50124 -0.88
480 621 5npk (B) 417 592 62.00 0 1 1.02408 -1.41
49 463 3zkb (B) 10 424 99.99 0 1 1.66833 -0.84
64 708 4i3h (A) 24 639 48.00 0 1 1.21576 0.71
465 714 5bs8 (B) 426 675 99.99 0 1 1.50124 -0.88
480 621 5npk (B) 417 592 62.00 0 1 1.02408 -1.41

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:

  • 2ZJT: Crystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation
  • Fu, G.S., Zhu, D.Y., Hu, Y.L., Wang, D.C.
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
    2.80 X-RAY DIFFRACTION 2962 494 2008-03-10 2009-03-10 2014-02-12
  • 3IG0: crystal structure of the second part of the Mycobacterium tuberculosis DNA gyrase reaction core: the TOPRIM domain at 2.1 A resolution
  • Piton, J., Aubry, A., Delarue, M., Mayer, C.
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
    2.10 X-RAY DIFFRACTION 1474 242 2009-07-27 2010-07-28 2017-11-01
  • 3M4I: Crystal structure of the second part of the Mycobacterium tuberculosis DNA gyrase reaction core: the TOPRIM domain at 1.95 A resolution
  • Piton, J., Petrella, S., Aubry, A., Mayer, C.
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
    1.95 X-RAY DIFFRACTION 1490 242 2010-03-11 2010-09-29 2011-07-13
  • Ligand information
  • (4S)-2-METHYL-2,4-PENTANEDIOL C[C@@H](CC(C)(C)O)O non-polymer Search in DB

Expression

Upregulation Percent Ranking Shows this level of upregulation in
This gene ranks in the mid 40-60% group of genes. Dormant phase.
Upregulation Percent Ranking Shows this level of upregulation in
This gene ranks in the lower 20-40% group of genes. Dormant phase.
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_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 this record   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

Rv0005 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu5 this record 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
  • 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
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
growth (GO:0040007) decreased (PATO:0000468) inferred from in vitro culture assay (ECO:0000182) Mycobacterium tuberculosis 95   535125   585111  
Annotator: crowther@u.washington.edu. Comment: 2007-12-04. References: 3919625
growth (GO:0040007) drug insensitive (PATO:0000528) inferred from in vitro culture assay (ECO:0000182) Mycobacterium tuberculosis 95   2349   55808   411040   411133   535125   547180   585111  
Annotator: crowther@u.washington.edu. Comment: 2007-12-04. References: 16377674
catalytic activity (GO:0003824) drug insensitive (PATO:0000528) in vitro (MI:0492) inferred from enzyme assay (ECO:0000005) Mycobacterium tuberculosis 95   2349   55808   411040   411133   535125   547180   585111  
Annotator: crowther@u.washington.edu. Comment: 2007-12-04. References: 16377674

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 log in using your TDR Targets username and password and send them to us using the corresponding form in this page (only visible to registered users) or 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

Compound Source Reference
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) DNA gyrase subunit B Compounds References
Escherichia coli DNA gyrase, subunit B Compounds References
Streptococcus pneumoniae ParE Compounds References
Leishmania major mitochondrial DNA topoisomerase II Compounds References
Mycobacterium smegmatis DNA gyrase subunit B Compounds References
Plasmodium falciparum DNA gyrase subunit B Compounds References
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) DNA gyrase subunit B Compounds References
Staphylococcus aureus subsp. aureus Mu50 DNA gyrase Compounds References
Staphylococcus aureus DNA gyrase subunit B Compounds References
Staphylococcus aureus DNA topoisomerase 4 subunit B Compounds References
Trypanosoma cruzi mitochondrial DNA topoisomerase II, putative 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 53.0% 661 aa Compounds References
Staphylococcus aureus Topoisomerase IV 663 aa 46.6% 670 aa Compounds References

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.1444 0.4208 0
0.0533 0.5291 0.4508
0.2291 0.496 0.4957
0.0836 0.2518 0.4296
0.0832 0.6424 0.6412
0.044 0.3982 0.3924
0.0181 0.3344 0.3009
0.0532 0.4846 0.4844
0.0312 0.3502 0.3816
0.1985 0.4682 0.4682
0.1694 0.5708 0.5696
0.2979 0.7657 0
0.0809 0.7186 0.7158
0.0306 0.8532 1
0.0532 0.4846 0.4844
0.0847 0.6424 0.6412
0.0155 0.4208 0
0.0153 0.378 0
0.0463 0.4145 0.4082
0.0183 0.3222 0.3222
0.0132 0.4114 0.3786
0.0819 0.3003 0.4274
0.0193 0.3487 0
0.272 0.4445 1
0.1908 0.478 0.4759
0.0153 0.378 0
0.272 0.4445 1
0.1085 0.6467 0.6467
0.3709 0.5573 0.5573
0.0501 0.55 0
0.0153 0.378 0
0.1254 0.4765 0.4758
0.0832 0.6424 0.6412
0.0584 0.5454 0
0.3478 0.4641 0.4637
0.1444 0.4208 0
0.3201 0.5709 0.5701
0.062 0.5052 0
0.0191 0.3149 0.2591
0.1405 0.4323 0
0.0149 0.4831 0.4523
0.0131 0.2784 0.3925
0.0153 0.2946 0.4867
0.1647 0.6425 0.6421
0.1192 0.6193 0.6157
0.0306 0.3424 1
0.1266 0.4378 0
0.0251 0.2608 0.419
0.1274 0.4364 0.4364
0.0306 0.3119 1
0.1048 0.4208 0
0.1254 0.4765 0.4758
0.1399 0.4796 0.4796
0.0602 0.4585 0
0.0153 0.378 0
0.0153 0.3335 0.3766
0.0153 0.2992 0.5077
0.1263 0.4801 0.4799
0.0531 0.4572 0
0.1341 0.605 0.6032
0.0591 0.4099 0.4044
0.5061 0.5404 0.5404
0.0306 0.7743 1
0.0153 0.3709 0
0.0153 0.8688 1
0.1166 0.6834 0.6806
0.0247 0.4121 0
0.1321 0.4529 0
0.0306 0.3776 1
0.0683 0.4248 0
0.0153 0.378 0
0.1303 0.6043 0.6018
0.0697 0.4182 0
0.272 0.4445 1
0.0815 0.7186 0.7147
0.0153 0.6322 0.5
0.1812 0.4748 0.4742
0.2998 0.573 0.5729
0.1392 0.4639 0
0.1908 0.478 0.4759
0.5355 0.276 0.5302
0.0307 0.3944 0.3938
0.0153 0.2818 0.5
0.0188 0.8101 0.8101
0.0131 0.4208 0
0.1263 0.4801 0.4799
0.106 0.4455 0
0.1647 0.6425 0.6421
0.1123 0.4144 0
0.0132 0.7606 1
0.1647 0.6425 0.6421
0.0168 0.3858 1
0.344 0.5654 0.5654
0.0815 0.3269 1
0.0153 0.378 0
0.1343 0.4715 0
0.1647 0.6425 0.6421
0.3057 0.5776 0.5776
0.0506 0.2989 1
0.5355 0.276 0.5302
0.014 0.4388 0
0.2229 0.6142 0.6141
0.1066 0.4778 0.475
0.0153 0.5612 0.5
0.0249 0.4241 0.4089
0.0306 0.3769 0.6589
0.1372 0.4208 0
0.1647 0.6425 0.6421
0.1263 0.4801 0.4799
0.1908 0.478 0.4759
0.272 0.4445 1
0.0072 0.4707 0
0.02 0.3483 0.3928
0.0195 0.3149 0.3059
0.0852 0.6424 0.6412
0.0515 0.4983 0
0.0847 0.6442 0.6412
0.0153 0.5288 0.7249
0.0183 0.3054 0
0.126 0.4554 0.4554
0.1791 0.4635 0
0.5071 0.5329 0.5329
0.0136 0.3818 0
0.0857 0.6443 0.6413
0.0306 0.3712 0.5
0.6001 0.5287 0.5287
0.4702 0.5417 0.5417
0.16 0.437 0
0.1976 0.4954 0.4938
0.0366 0.4669 0

Assayability

Assay information

No assay information for this target.

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Rv0005 cloned gene BRENDA A gene with this EC number or name or sequence has been cloned from Mycobacterium smegmatis ( 1 )

Bibliographic References

46 literature references were collected for this gene.

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Gene identifier Rv0005 (Mycobacterium tuberculosis), DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase)
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