Sandbox Reserved 828: Difference between revisions

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~~{{STRUCTURE_1ab4| PDB~~=1ab4 ~~| SCENE~~= }}

[[Image:1ab4.png|left|200px]]

'''Introduction :'''

Gyrase is the only prokaryote DNA topoisomerase II able to introduce negative supercoils in the DNA in order to remove positive supercoils. It catalyses the hydrolysis of two phosphodiester bonds in a DNA segment (called G segment). Then, thanks to ATP dependant conformation changes it enables the passage of another segment (the T segment) through the break, and then religates the broken segment. Gyrase acts prior to the replication (before the replication fork) or other mecanisms requiring loose DNA. In abscence of ATP, like other topoisomerases II, gyrase only relaxes supercoils.

Gyrase is the '''only prokaryote DNA topoisomerase II able to introduce negative supercoils in the DNA''' in order to remove positive supercoils. It '''catalyses the hydrolysis of two phosphodiester bonds in a DNA segment''' (called G segment). Then, thanks to '''ATP dependant conformation changes''' it enables the passage of another segment (the T segment) through the break, and then religates the broken segment. Gyrase acts prior to the replication (before the replication fork) or other mecanisms requiring loose DNA.

'''In abscence of ATP, like other topoisomerases II, gyrase only relaxes supercoils.'''

Gyrase is coded by two differents contiguous genes gyrA and GgyrB as it is a 350 kDa A2B2 heterotetramers of two A proteins and two B proteins.

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The structures formed a novel beta barrel, which bends DNA by wrapping the nucleic acid around itself. The bending of DNA by gyrase has been proposed as a key mechanism in the ability of gyrase to introduce negative supercoils into the DNA. This is consistent with footprinting data that shows

that gyrase has a 140-base-pair footprint. Both gyrase and topoisomerase IV CTDs bend DNA, but only gyrase introduces negative supercoils.

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'''Reaction'''

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.

Sandbox Reserved 828: Difference between revisions

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@@ Line 4: / Line 4: @@
 ----
-{{STRUCTURE_1ab4|  PDB=1ab4  |  SCENE=  }}
+<Structure load='1ab4' size='400' frame='true' align='right' caption='Breakage/Reunion domain at 2.8Å' scene='Insert optional scene name here' />
 [[Image:1ab4.png|left|200px]]
 '''Introduction :'''
-Gyrase is the only  prokaryote DNA topoisomerase II able to introduce negative supercoils in the DNA in order to remove positive supercoils. It catalyses the hydrolysis of two phosphodiester bonds in a DNA segment (called G segment). Then, thanks to ATP dependant conformation changes it enables the passage of another segment (the T segment) through the break, and then religates the broken segment. Gyrase acts prior to the replication (before the replication fork) or other mecanisms requiring loose DNA. In abscence of ATP, like other topoisomerases II, gyrase only relaxes supercoils.
+Gyrase is the '''only  prokaryote DNA topoisomerase II able to introduce negative supercoils in the DNA''' in order to remove positive supercoils. It '''catalyses the hydrolysis of two phosphodiester bonds in a DNA segment''' (called G segment). Then, thanks to '''ATP dependant conformation changes''' it enables the passage of another segment (the T segment) through the break, and then religates the broken segment. Gyrase acts prior to the replication (before the replication fork) or other mecanisms requiring loose DNA.
+'''In abscence of ATP, like other topoisomerases II, gyrase only relaxes supercoils.'''
 Gyrase is coded by two differents contiguous genes gyrA and GgyrB as it is a 350 kDa A2B2 heterotetramers of two A proteins and two B proteins.
@@ Line 27: / Line 28: @@
 The structures formed a novel beta barrel, which bends DNA by wrapping the nucleic acid around itself. The bending of DNA by gyrase has been proposed as a key mechanism in the ability of gyrase to introduce negative supercoils into the DNA. This is consistent with footprinting data that shows
 that gyrase has a 140-base-pair footprint. Both gyrase and topoisomerase IV CTDs bend DNA, but only gyrase introduces negative supercoils.
+----
+'''Reaction'''
+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.