User:Jonathan Lloyd/Sandbox 1
From Proteopedia
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The bromodomain of ATAD2b is comprosied of 71 amino acids including 18 of the 20 main residues (excluding glutamine and tryptophan). The bromodomain is alpha helical except at the 2 loops where it is random coil. It is globular and typically resides in its monomer form. | The bromodomain of ATAD2b is comprosied of 71 amino acids including 18 of the 20 main residues (excluding glutamine and tryptophan). The bromodomain is alpha helical except at the 2 loops where it is random coil. It is globular and typically resides in its monomer form. | ||
Since much is unknown about ATAD2b we look to its paralogue ATAD2a which has been the focus of many studies. ATAD2a and ATAD2b both share the AAA and bromodomain, in which they are 97% and 74% identical respectively. identical and Based on the observed high sequence similarity with well characterized bromodomains, the ATAD2b bromodomain is expected to recognize acetylated lysine. However since no tests have yet to be done on this additional studies are needed to identify the exact modifications that the ATAD2b bromodomain may recognize. Throughout all bromodomains it seems as though there are very important residues that reside in the binding pocket, Tyr760, Tyr802 and Asn803. These three amino acids are highly conserved and thus must have a major impact in the binding pocket, they are most likely the key to bromodomains binding to acetylated lysine modifications. | Since much is unknown about ATAD2b we look to its paralogue ATAD2a which has been the focus of many studies. ATAD2a and ATAD2b both share the AAA and bromodomain, in which they are 97% and 74% identical respectively. identical and Based on the observed high sequence similarity with well characterized bromodomains, the ATAD2b bromodomain is expected to recognize acetylated lysine. However since no tests have yet to be done on this additional studies are needed to identify the exact modifications that the ATAD2b bromodomain may recognize. Throughout all bromodomains it seems as though there are very important residues that reside in the binding pocket, Tyr760, Tyr802 and Asn803. These three amino acids are highly conserved and thus must have a major impact in the binding pocket, they are most likely the key to bromodomains binding to acetylated lysine modifications. | ||
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== Sequence Analysis == | == Sequence Analysis == | ||
A BLAST search of the bromodomain in ATAD2b yields many other bromodomain-containing proteins. In the table below are 8 other proteins that contain a bromodomain. Their sequences were aligned to ATAD2b using Clustal Omega and show the percent identity and similarity to ATAD2b. You can see the conserved residues throughout all the proteins (marked with *), there are 13 out of the 71 residues or 18.3%. Many of the identical residues are a result of these 13 residues showing how highly conserved they are. They have very important function in the bromodomain which is why it would be expected to see the same residues in all bromodomains. The closest protein to ATAD2b is ATAD2a which is no surprise considering they are paralogues of each other. | A BLAST search of the bromodomain in ATAD2b yields many other bromodomain-containing proteins. In the table below are 8 other proteins that contain a bromodomain. Their sequences were aligned to ATAD2b using Clustal Omega and show the percent identity and similarity to ATAD2b. You can see the conserved residues throughout all the proteins (marked with *), there are 13 out of the 71 residues or 18.3%. Many of the identical residues are a result of these 13 residues showing how highly conserved they are. They have very important function in the bromodomain which is why it would be expected to see the same residues in all bromodomains. The closest protein to ATAD2b is ATAD2a which is no surprise considering they are paralogues of each other. | ||
| - | <Structure load='3dai' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /> | ||
[[Image:table 1.png]] | [[Image:table 1.png]] | ||
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== AAA ATPase Domain == | == AAA ATPase Domain == | ||
The AAA domains share a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein, which exert their activity through the energy-dependent remodeling or translocation of macromolecules. Members of the AAA family are found in all organisms and they are essential for many cellular functions. They are involved in processes such as DNA replication, protein degradation, membrane fusion, microtubule severing, peroxisome biogenesis, signal transduction and the regulation of gene expression. ATP hydrolysis by AAA ATPases involves a nucleophilic attack on the ATP gamma-phosphate by an activated water molecule, leading to movement of the N-terminal and C-terminal AAA subdomains relative to each other. This movement allows the exertion of mechanical force, amplified by other ATPase domains within the same oligomeric structure. The AAA domain is part of the P-loop containing nucleoside triphosphate hydrolases superfamily which mainly consists of beta sheets. | The AAA domains share a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein, which exert their activity through the energy-dependent remodeling or translocation of macromolecules. Members of the AAA family are found in all organisms and they are essential for many cellular functions. They are involved in processes such as DNA replication, protein degradation, membrane fusion, microtubule severing, peroxisome biogenesis, signal transduction and the regulation of gene expression. ATP hydrolysis by AAA ATPases involves a nucleophilic attack on the ATP gamma-phosphate by an activated water molecule, leading to movement of the N-terminal and C-terminal AAA subdomains relative to each other. This movement allows the exertion of mechanical force, amplified by other ATPase domains within the same oligomeric structure. The AAA domain is part of the P-loop containing nucleoside triphosphate hydrolases superfamily which mainly consists of beta sheets. | ||
Revision as of 22:39, 9 December 2015
ATAD2b
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