Sandbox Reserved 828: Difference between revisions
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Gyrase is the '''only prokaryote DNA topoisomerase II able to introduce negative supercoils in the DNA''' (see [http://en.wikipedia.org/wiki/DNA_supercoil DNA Supercoil]) in order to remove positive supercoils. It '''catalyses the hydrolysis of two phosphodiester bonds in a DNA segment (DNA cleavage)''' | Gyrase is the '''only prokaryote DNA topoisomerase II able to introduce negative supercoils in the DNA''' (see [http://en.wikipedia.org/wiki/DNA_supercoil DNA Supercoil]) in order to remove positive supercoils. It '''catalyses the hydrolysis of two phosphodiester bonds in a DNA segment (DNA cleavage)''' called G segmen. 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.''' | '''In abscence of ATP, like other topoisomerases II, gyrase only relaxes supercoils.''' | ||
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The gyrA 59kDa N-ter domain is called Breakage and reunion domain. It is composed of two domains at the <scene name='56/568026/Head/2'>head</scene> region : | The gyrA 59kDa N-ter domain is called Breakage and reunion domain. It is composed of two domains at the <scene name='56/568026/Head/2'>head</scene> region : | ||
a winged-helix-turn-helix domain or <scene name='56/568026/Whd/1'>winged helix domain (WHD</scene>) where lies the catalytic tyrosines: the active-site tyrosines <scene name='56/568026/Tyr122/1'>(Tyr 122)</scene> are on loops at either end of the dimer interface. | *a winged-helix-turn-helix domain or <scene name='56/568026/Whd/1'>winged helix domain (WHD</scene>) where lies the catalytic tyrosines: the active-site tyrosines <scene name='56/568026/Tyr122/1'>(Tyr 122)</scene> are on loops at either end of the dimer interface. | ||
a <scene name='56/568026/Tower/1'>tower domain</scene> with alpha/beta structure that participates in DNA bending during cleavage. | *a <scene name='56/568026/Tower/1'>tower domain</scene> with alpha/beta structure that participates in DNA bending during cleavage. | ||
The ‘head’ dimer interface is dominated by an antiparallel side by-side packing of the <scene name='56/568026/Alpha3/2'>alpha 3</scene> (the first helix of the HTH motif) from each monomer, together with their adjoining loops. At the top of the interface, the ‘recognition’ helices <scene name='56/568026/Alpha4/1'>alpha4</scene> make a head-to-head antiparallel dimer contact. | The ‘head’ dimer interface is dominated by an antiparallel side by-side packing of the <scene name='56/568026/Alpha3/2'>alpha 3</scene> (the first helix of the HTH motif) from each monomer, together with their adjoining loops. At the top of the interface, the ‘recognition’ helices <scene name='56/568026/Alpha4/1'>alpha4</scene> make a head-to-head antiparallel dimer contact. | ||
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# Gyrase binds DNA (gyrase binds more strongly to relaxed or linear DNA than to supercoiled one by a factor of about ten) | # 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 | # Cleavage of the G-segment | ||
# Passage of T-segment of the other strand through the cleavage site (thanks to | # Passage of T-segment of the other strand through the cleavage site (thanks to ATP) | ||
# Reunion of the G segment | # Reunion of the G segment | ||
# Translocation | # Translocation | ||
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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 ( | The cleavage of DNA is achieved by a '''transesterification reaction between the tyrosines <scene name='56/568026/Tyr122/1'>(Tyr 122)</scene> 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 '''active site tyrosines <scene name='56/568026/Tyr122/1'>(Tyr 122)</scene>''' 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 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. | ||
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==See Also== | ==See Also== | ||
*[[Gyrase|Gyrase]] | *[[Gyrase|Gyrase]] | ||
*[[Topoisomerase|Topoisomerase]] | |||
==Reference== | ==Reference== | ||
