Sandbox Reserved 828: Difference between revisions

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=='''Reaction'''==
=='''Reaction'''==


The gyrase binds more strongly to relaxed or linear DNA than to supercoiled one by a factor of about ten.
The process of DNA supercoiling by gyrase is the following :
 
# gyrase binds DNA (gyrase binds more strongly to relaxed or linear DNA than to supercoiled one by a factor of about ten)
 
# cleavage of the G-segment
 
# passage of T-segment of the other strand through the cleavage site (thanks to DNA)
 
# Reunion of the G segment
The cleavage of DNA is achieved by a '''transesterification reaction between the tyrosines (Tyr122) and the target phosphoryl groups on opposing strands of the DNA backbone''', resulting in the tyrosine being covalentlty attached to the 5' end of the cleaved segment with a 4-base overhang.
# Translocation
The '''active site tyrosines (Tyr 122)''' are on loops at either end of the dimer interface, 30Å apart, and sit at the ends of strongly basic grooves created by the dimer-related monomers.
 
The gyrase structure reveals a '''new cluster of conserved residues''', juxtaposing Tyr 122 and Arg 121 from one monomer and His 80, Arg 32 and Lys 42 from the other monomer. '''This cluster may form the active site of the breakage–reunion reaction''', with the other conserved positive charges (Arg 46 and Arg 47) anchoring the non-covalently bound 3' end of the cleaved DNA.


The A subunit is responsible for the breakage reunion of DNA whereas the B-subunit has the ATPase activity.
The A subunit is responsible for the breakage reunion of DNA whereas the B-subunit has the ATPase activity.
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* DNA cleavage (induced by Quinolone)
* DNA cleavage (induced by Quinolone)
* Unknotting DNA strands
* Unknotting DNA strands
Contrary to the introduction of negative supercoils, some of these reactions don't necessarily need the energy from ATP-hydrolysis.
Contrary to the introduction of negative supercoils, some of these reactions don't necessarily need the energy from ATP-hydrolysis.
The cleavage of DNA is achieved by a '''transesterification reaction between the tyrosines (Tyr122) and the target phosphoryl groups on opposing strands of the DNA backbone''', resulting in the tyrosine being covalentlty attached to the 5' end of the cleaved segment with a 4-base overhang.
The '''active site tyrosines (Tyr 122)''' are on loops at either end of the dimer interface, 30Å apart, and sit at the ends of strongly basic grooves created by the dimer-related monomers.
The gyrase structure reveals a '''new cluster of conserved residues''', juxtaposing Tyr 122 and Arg 121 from one monomer and His 80, Arg 32 and Lys 42 from the other monomer. '''This cluster may form the active site of the breakage–reunion reaction''', with the other conserved positive charges (Arg 46 and Arg 47) anchoring the non-covalently bound 3' end of the cleaved DNA.
The gyrase could be inhibited by both the quinolones and the coumarins.
The gyrase could be inhibited by both the quinolones and the coumarins.
Coumarins prevent the B-subunit of the gyrase from hydrolyzing the ATP, so that the gyrase can't come back to its starting state for another round of supercoiling. The mecanism is not yet well known.
Coumarins prevent the B-subunit of the gyrase from hydrolyzing the ATP, so that the gyrase can't come back to its starting state for another round of supercoiling. The mecanism is not yet well known.
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There are also others antibiotics, like the Cinodine which binds DNA and inhibits its supercoiling by gyrase.
There are also others antibiotics, like the Cinodine which binds DNA and inhibits its supercoiling by gyrase.
    
    
==See Also==
==See Also==
*[[Gyrase|Gyrase]]
*[[Gyrase|Gyrase]]
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