User:Elizabeth Cook/Sandbox 1: Difference between revisions

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Bromodomains are composed of 4 alpha helices (<scene name='10/1079536/Helix/1'>αZ, αA, αB, αC)</scene>, and 2 loops (ZA and BC). There are typically 4 conserved water molecules found within the acetyllysine binding pocket of the bromodomain. The two loops contain the majority of the residues responsible for ligand coordination, including the <scene name='10/1079536/N514_part_2/1'>conserved asparagine</scene>, N514 for CECR2, located in the BC loop. In addition, there is a hydrophobic shelf found before the before the ZA loop and following αZ helix (WPF in CECR2). There is also a <scene name='10/1079536/Gatekeeper/1'>gatekeeper residue</scene> that corresponds to the first residue found in the αC that is usually hydrophobic, although it is Y520 in CECR2. Histone acetyllysines form a hydrogen bond with the conserved asparagine of bromodomains while various other residues make polar contacts to stabilize the interaction, directly or indirectly.<ref>PMID:27769355</ref>
Bromodomains are composed of 4 alpha helices (<scene name='10/1079536/Helix/1'>αZ, αA, αB, αC)</scene>, and 2 loops (ZA and BC). There are typically 4 conserved water molecules found within the acetyllysine binding pocket of the bromodomain. The two loops contain the majority of the residues responsible for ligand coordination, including the <scene name='10/1079536/N514_part_2/1'>conserved asparagine</scene>, N514 for CECR2, located in the BC loop. In addition, there is a hydrophobic shelf found before the before the ZA loop and following αZ helix (WPF in CECR2). There is also a <scene name='10/1079536/Gatekeeper/1'>gatekeeper residue</scene> that corresponds to the first residue found in the αC that is usually hydrophobic, although it is Y520 in CECR2. Histone acetyllysines form a hydrogen bond with the conserved asparagine of bromodomains while various other residues make polar contacts to stabilize the interaction, directly or indirectly.<ref>PMID:27769355</ref>


While there is no solved structure for histone bound, we can assume (ref)
While there is no solved structure for histone bound CECR2, it can be assumed that it binds in a similar fashion to other bromodomains, considering the high levels of conservation amongst bromodomain-containing proteins.
   
   


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