Sandbox reserved 1752: Difference between revisions
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In total, there are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures, such as PcrA, Rep, and Srs2. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD [1]. | In total, there are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures, such as PcrA, Rep, and Srs2. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD [1]. | ||
== UvrD Binding Site for ATP analog (AMPPNP) == | == UvrD Binding Site for ATP analog (AMPPNP) == | ||
When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/ | When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/3'>ATP analog</scene> so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.The green ion shown in the ATP analog scene is a Mg<sup>2+</sup> ion, which is essential for ATP hydrolysis and interacts with the β and γ phosphates. The magnesium ion is surrounded by essential residues that when altered, have been shown to have reduced ATPase activity [1]. | ||
== UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) == | == UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) == | ||
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/2'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycogen molecule, which has similar binding that the DNA backbone has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used as a model 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/2'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycogen molecule, which has similar binding that the DNA backbone has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used as a model 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]. | ||
