Sandbox reserved 1752: Difference between revisions
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To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycogen molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycogen molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP [1]. | To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycogen molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycogen molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP [1]. | ||
== Separation Pin == | == Separation Pin == | ||
The "<scene name='92/925553/Pin_complex/1'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so | The "<scene name='92/925553/Pin_complex/1'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so UvrD can unwind more DNA. The separation pin also prevents ssDNA once unwound from moving backwards and from reannealing. The proposed method is called the wrench-and-inchworm method, which is when the enzyme binds DNA and attaches at different points and then moves 1 nucleotide per ATP molecule.After an ATP molecule is released, UvrD is then ready to proceed forward to the next nucleotide [1]. | ||
== References == | == References == | ||
{{Reflist}} | {{Reflist}} | ||
