Cloned (Comment) | Organism |
---|---|
Mycobacterium tuberculosis encodes only one type II topoisomerase, i.e. DNA gyrase, recombinant expression of wild-type and mutant enzymes | Mycobacterium tuberculosis |
Crystallization (Comment) | Organism |
---|---|
recombinant engineered DNA gyrase GyrBA57 in apo- and AMPPNP-bound forms, sitting-drop vapour diffusion method, mixing of 10 mg/mlGyrBA57 in presence or absence of Mg2+ or 5 mM MgCl2 plus 2.5 mM AMPPNP, or in the presence of 1 mM AMPPNP plus 8 mM oligonucleotides, with 100 mM sodium acetate, 100 mM MES, pH 6.5, 26% PEG 400, 25% ethylene glycol, and 10 mM MgCl2 (for Apo-GyrBA57 and AMPPNP-bound GyrBA57, respectively), X-ray diffraction structure determination and analysis at 2.6 A and 3.3 A resolution, respectively | Mycobacterium tuberculosis |
Protein Variants | Comment | Organism |
---|---|---|
D211K/E212K/E213K/E214K | site-directed mutagenesis, the GyrBAKKKK mutant comprises the charge-reversal mutation of all the acidic residues composing the DEEE loop into basic ones (211DEEE214 into 211KKKK214) | Mycobacterium tuberculosis |
E221K/D225K/E228K/R236E/H244A | site-directed mutagenesis, mutant GyrBAmC-loop, the substitution of five residues in the C-loop which are implicated in salt bridges or strong hydrogen interactions participating to the stabilization of the N-gate extremely open conformation | Mycobacterium tuberculosis |
additional information | the subunits GyrB and GyrA57 are linked into a single polypeptide chain (termed GyrBA57) leading to an enzyme (full-length GyrB-GyrA57)2 with a total molecular weight of almost 260 kDa (by analytical ultracentrifugation) and four ATPases domains. Construction of the GyrBA57DELTAC-loop truncated mutant. The two GyrBA57 and GyrBA57DC-loop enzymes are dimeric in solution. Structure modelling | Mycobacterium tuberculosis |
KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
0.3 | - |
ATP | enzyme mutant GyrBADELTAC-loop, pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.7 | - |
ATP | enzyme mutant GyrBAmC-loop (E221K/D225K/E228K/R236E/H244A), pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.7 | - |
ATP | wild-type enzyme GyrBA, pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.75 | - |
ATP | enzyme dimeric mutant GyrBA57DELTAC-loop, pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.8 | - |
ATP | enzyme dimeric mutant GyrBA57, pH 7.5, 30°C | Mycobacterium tuberculosis | |
1 | - |
ATP | enzyme mutant GyrBAKKK (D211K/E212K/E213K/E214K), pH 7.5, 30°C | Mycobacterium tuberculosis |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
ATP + H2O | Mycobacterium tuberculosis | - |
ADP + phosphate | - |
? | |
ATP + H2O | Mycobacterium tuberculosis H37Rv | - |
ADP + phosphate | - |
? | |
ATP + H2O | Mycobacterium tuberculosis ATCC 25618 | - |
ADP + phosphate | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Mycobacterium tuberculosis | P9WG47 AND P9WG45 | subunits a and b | - |
Mycobacterium tuberculosis ATCC 25618 | P9WG47 AND P9WG45 | subunits a and b | - |
Mycobacterium tuberculosis H37Rv | P9WG47 AND P9WG45 | subunits a and b | - |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
ATP + H2O | - |
Mycobacterium tuberculosis | ADP + phosphate | - |
? | |
ATP + H2O | - |
Mycobacterium tuberculosis H37Rv | ADP + phosphate | - |
? | |
ATP + H2O | - |
Mycobacterium tuberculosis ATCC 25618 | ADP + phosphate | - |
? | |
additional information | negative DNA supercoiling activity assays using relaxed pBR322 DNA as substrate, and ATPase assays | Mycobacterium tuberculosis | ? | - |
- |
|
additional information | negative DNA supercoiling activity assays using relaxed pBR322 DNA as substrate, and ATPase assays | Mycobacterium tuberculosis H37Rv | ? | - |
- |
|
additional information | negative DNA supercoiling activity assays using relaxed pBR322 DNA as substrate, and ATPase assays | Mycobacterium tuberculosis ATCC 25618 | ? | - |
- |
Subunits | Comment | Organism |
---|---|---|
heterodimer | subunits GyrB and GyrA57 | Mycobacterium tuberculosis |
More | quaternary organization and interdomain connections of full-length (GyrB-GyrA57)2 gyrase, structure analysis, detailed overview | Mycobacterium tuberculosis |
Synonyms | Comment | Organism |
---|---|---|
ATPase | - |
Mycobacterium tuberculosis |
DNA gyrase | - |
Mycobacterium tuberculosis |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
30 | - |
ATPase assay at | Mycobacterium tuberculosis |
37 | - |
negative DNA supercoiling activity assay at | Mycobacterium tuberculosis |
Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
0.05 | - |
ATP | wild-type enzyme GyrBA, pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.06 | - |
ATP | enzyme dimeric mutant GyrBA5, pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.06 | - |
ATP | enzyme dimeric mutant GyrBA57DELTAC-loop, pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.08 | - |
ATP | enzyme mutant GyrBAmC-loop (E221K/D225K/E228K/R236E/H244A), pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.09 | - |
ATP | enzyme mutant GyrBAKKK (D211K/E212K/E213K/E214K), pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.11 | - |
ATP | enzyme mutant GyrBADELTAC-loop, pH 7.5, 30°C | Mycobacterium tuberculosis |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.5 | - |
assay at | Mycobacterium tuberculosis |
General Information | Comment | Organism |
---|---|---|
additional information | the C-loop (residues 214-245), a Corynebacteriales-specific GyrB insert, stabilizes the a specific open N-gate conformation of the enzyme, structure overview. The N-gate of GyrBA57 (Mtb) gyrase lies in an extremely open conformation. The C-loop plays a role in the ATPase activity of the enzyme. The open N-gate state persists even in the DNA-free gyrase-AMPPNP complex and an unexpected connection between the ATPase and cleavage core domains mediated by two Corynebacteriales-specific motifs, respectively, the C-loop and DEEE-loop. The C-loop participates in the stabilization of this open conformation, explaining why this gyrase has a lower ATPase activity. Structure-function analysis, ATPase domain structure | Mycobacterium tuberculosis |
physiological function | type II DNA topoisomerases are ubiquitous enzymes that manage DNA reorganization, and are therefore essential for many cellular events that take place during cell life. Using ATP as a cofactor, they control DNA topology by adding or removing DNA supercoils and by tangling or knotting DNA. Topoisomerases achieve these topological rearrangements through a succession of dissociation/association events of three domain-dimerization interfaces, which function as open/closed gates, to allow the movement of one DNA duplex through another | Mycobacterium tuberculosis |
kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
0.071 | - |
ATP | wild-type enzyme GyrBA, pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.075 | - |
ATP | enzyme dimeric mutant GyrBA5, pH 7.5, 30°C, pH 7.5, 30°C7 | Mycobacterium tuberculosis | |
0.08 | - |
ATP | enzyme dimeric mutant GyrBA57DELTAC-loop, pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.09 | - |
ATP | enzyme mutant GyrBAKKK (D211K/E212K/E213K/E214K), pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.114 | - |
ATP | enzyme mutant GyrBAmC-loop (E221K/D225K/E228K/R236E/H244A), pH 7.5, 30°C | Mycobacterium tuberculosis | |
0.367 | - |
ATP | enzyme mutant GyrBADELTAC-loop, pH 7.5, 30°C | Mycobacterium tuberculosis |