Factor Xa: Difference between revisions
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====Helix capping ==== | ====Helix capping ==== | ||
Helices have exposed hydrogen bond donors from the first 4 residues at the N-terminus. Helix capping refers to H-bonding to these groups, primarily by nearby side chains, to "seal" the helix. Factor Xa forms a helix from residue 165-171 that is capped at the N-terminus by an aspartate residue number 164. The aspartate side chain is twisted to follow the helix and provide capping. The backbone carbonyl is hydrogen bonded to the backbone nitrogen groups of serine 167 and cysteine 168. One of the side chain oxygen groups of aspartate forms hydrogen bonds with the backbone nitrogen groups of asparagine 166 and serine 167. Arginine 165 is the first residue in the helix and it provides capping hydrogen bonds for lysine 169. The backbone nitrogen group of arginine 165 appears to form a hydrogen bond with the solvent. The aspartate and asparagine residues 164 and 165 provide capping hydrogen bonds for the hydrogen bond donors of the first 4 N-terminal helix residues. | Helices have exposed hydrogen bond donors from the first 4 residues at the N-terminus. Helix capping refers to H-bonding to these groups, primarily by nearby side chains, to "seal" the helix. Factor Xa forms a helix from residue 165-171 that is capped at the N-terminus by an aspartate residue number 164. The aspartate side chain is twisted to follow the helix and provide capping. The backbone carbonyl is hydrogen bonded to the backbone nitrogen groups of serine 167 and cysteine 168. One of the side chain oxygen groups of aspartate forms hydrogen bonds with the backbone nitrogen groups of asparagine 166 and serine 167. Arginine 165 is the first residue in the helix and it provides capping hydrogen bonds for lysine 169. The backbone nitrogen group of arginine 165 appears to form a hydrogen bond with the solvent. The aspartate and asparagine residues 164 and 165 provide capping hydrogen bonds for the hydrogen bond donors of the first 4 N-terminal helix residues. | ||
===Activation peptide=== | |||
Chymotrypsin-like proteases are synthesized as inactive precursors (“zymogens”) containing N-terminal extensions. Four segments are deformed in the zymogens of chymotrypsin and trypsin: the N-terminus to residue 19, residues 142-152, 184-193, and 216- 223 (these regions are collectively termed the activation domain36). This deformed region includes the S1 site and oxyanion hole, which explains the low activity of the zymogen. Proteolytic processing activates the zymogen, releasing the N-terminal Ile16. The new N-terminus forms a buried salt bridge with Asp194, inducing a conformational change that orders the activation domain. The S1 site and oxyanion hole are formed, creating the active protease. | |||
==Enzyme Mechanism== | ==Enzyme Mechanism== | ||
