User:Ann Taylor/Sandbox Trypsin
From Proteopedia
(Difference between revisions)
| Line 4: | Line 4: | ||
One of the ways we know about the mechanism of enzymes is through the use of xray crystallography structures of trapped intermediates or inhibitors bound to enzymes. In a paper by Radisky and Koshland<ref>PMID: 16636277</ref>, an acyl intermediate of trypsin (PDB code [[2AGG]] was characterized. | One of the ways we know about the mechanism of enzymes is through the use of xray crystallography structures of trapped intermediates or inhibitors bound to enzymes. In a paper by Radisky and Koshland<ref>PMID: 16636277</ref>, an acyl intermediate of trypsin (PDB code [[2AGG]] was characterized. | ||
| - | Serine proteases use a covalent mechanism to catalyze the hydrolysis of a peptide bond. A covalent bond is formed between <scene name='72/725330/Ser195/1'>Ser195</scene> and a substrate <scene name='72/725330/Substrate_and_ser/1'>peptide</scene>. | + | Serine proteases use a covalent mechanism to catalyze the hydrolysis of a peptide bond. A covalent bond is formed between <scene name='72/725330/Ser195/1'>Ser195</scene> and a substrate <scene name='72/725330/Substrate_and_ser/1'>peptide</scene>. The <scene name='72/725330/Ser_o_lys_bond_length/1'>distance</scene> between one of the Ser O configurations and the alpha carbon of the substrate lysine is the distance of a C-O bond, indicating that the covalent intermediate is indeed formed. There is a <scene name='72/725330/Water/2'>water</scene> situated in the active site, primed to cleave the acyl intermediate by the same <scene name='72/725330/Water_his_57/1'>histidine</scene> that participates in the catalytic triad. |
Specificity of the proteases is determined by a binding pocket. | Specificity of the proteases is determined by a binding pocket. | ||
Revision as of 04:37, 18 February 2016
The Mechanism of Trypsin
| |||||||||||
