User:James D Watson/Structural Templates: Difference between revisions

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Moving away from secondary structure elements, loop and nests, another type of structural motif is that of enzyme active sites. These structural motifs are usually more difficult to detect as they can be discontinuous, often involving elements widely spaced along the sequence. One such example is that of the "catalytic triad" of the serine proteases.

Serine proteases are found in a number of organisms but common to their function is the hydrolysis of peptide bonds. These enzymes catalyse the reaction using a highly reactive serine residue to attack the carbonyl group of the backbone to be hydrolysed. The chemistry of this reaction and the regeneration of the active site, requires the presence of the Ser-His-Asp catalytic triad. In chymotrypsin these residues are (Ser-195, His-57 and Asp-102) whereas in the bacterial subtilisin the site is formed by (Ser-221, His-64 and Asp-32). These two proteins are evolutionary unrelated and this is the classic example of convergent evolution to solve the problem of peptide bond hydrolysis.

Serine proteases are found in a number of organisms but common to their function is the hydrolysis of peptide bonds. These enzymes catalyse the reaction using a highly reactive serine residue to attack the carbonyl group of the backbone to be hydrolysed. The chemistry of this reaction and the regeneration of the active site, requires the presence of the Ser-His-Asp catalytic triad. In chymotrypsin (PDB entry [[1ab9]]) these residues are (Ser-195, His-57 and Asp-102) whereas in the bacterial subtilisin (PDB entry [[1st2]]) the site is formed by (Ser-221, His-64 and Asp-32). These two proteins are evolutionary unrelated and this is the classic example of convergent evolution to solve the problem of peptide bond hydrolysis.

The detection of these types of motif is almost impossible by looking at the amino acid sequence: there is no evolutionary relationship to detect, the residues are ordered differently in the sequence, and the spacing between the residues also varies. These motifs can be detected relativeley easily using structural comparison, particularly ~~the~~ template-based motif detection algorithms ~~(some of which are listed in table 2 below)~~. The subtilisin and chymotrypsin ~~catalytic triads~~ are shown ~~superposed here~~ - note that the global folds of these two proteins are very different so the site could not have been detected using such methods.

The detection of these types of motif is almost impossible by looking at the amino acid sequence: there is no evolutionary relationship to detect, the residues are ordered differently in the sequence, and the spacing between the residues also varies. These motifs can be detected relativeley easily using structural comparison, particularly template-based motif detection algorithms. The subtilisin and chymotrypsin structures are shown side by side - note that the global folds of these two proteins are very different so the site could not have been detected using such methods. Click to see the catalytic triad in <scene name='User:James_D_Watson/Structural_Templates/Subtilisin_catalytic_triad/1'>subtilisin</scene> and chymotrypsin respectively.

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 Moving away from secondary structure elements, loop and nests, another type of structural motif is that of enzyme active sites. These structural motifs are usually more difficult to detect as they can be discontinuous, often involving elements widely spaced along the sequence. One such example is that of the "catalytic triad" of the serine proteases.
-Serine proteases are found in a number of organisms but common to their function is the hydrolysis of peptide bonds. These enzymes catalyse the reaction using a highly reactive serine residue to attack the carbonyl group of the backbone to be hydrolysed. The chemistry of this reaction and the regeneration of the active site, requires the presence of the Ser-His-Asp catalytic triad. In chymotrypsin these residues are (Ser-195, His-57 and Asp-102) whereas in the bacterial subtilisin the site is formed by (Ser-221, His-64 and Asp-32). These two proteins are evolutionary unrelated and this is the classic example of convergent evolution to solve the problem of peptide bond hydrolysis.
+Serine proteases are found in a number of organisms but common to their function is the hydrolysis of peptide bonds. These enzymes catalyse the reaction using a highly reactive serine residue to attack the carbonyl group of the backbone to be hydrolysed. The chemistry of this reaction and the regeneration of the active site, requires the presence of the Ser-His-Asp catalytic triad. In chymotrypsin (PDB entry [[1ab9]]) these residues are (Ser-195, His-57 and Asp-102) whereas in the bacterial subtilisin (PDB entry [[1st2]]) the site is formed by (Ser-221, His-64 and Asp-32). These two proteins are evolutionary unrelated and this is the classic example of convergent evolution to solve the problem of peptide bond hydrolysis.
-The detection of these types of motif is almost impossible by looking at the amino acid sequence: there is no evolutionary relationship to detect, the residues are ordered differently in the sequence, and the spacing between the residues also varies. These motifs can be detected relativeley easily using structural comparison, particularly the template-based motif detection algorithms (some of which are listed in table 2 below). The subtilisin and chymotrypsin catalytic triads are shown superposed here - note that the global folds of these two proteins are very different so the site could not have been detected using such methods.
+The detection of these types of motif is almost impossible by looking at the amino acid sequence: there is no evolutionary relationship to detect, the residues are ordered differently in the sequence, and the spacing between the residues also varies. These motifs can be detected relativeley easily using structural comparison, particularly template-based motif detection algorithms. The subtilisin and chymotrypsin structures are shown side by side - note that the global folds of these two proteins are very different so the site could not have been detected using such methods. Click to see the catalytic triad in <scene name='User:James_D_Watson/Structural_Templates/Subtilisin_catalytic_triad/1'>subtilisin</scene> and chymotrypsin respectively.
+<applet load='1st2' size='300' frame='true' align='left' caption='Subtilisin 1st2' scene='User:James_D_Watson/Structural_Templates/Subtilisin_start/1'/>