Factor Xa: Difference between revisions
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The members of the trypsin-like serine protease family have two homologous greek key β-barrel subdomains (<scene name='Factor_Xa/Transparent_-no_inhib-_barrel1/1'>barrel 1</scene>, <scene name='Factor_Xa/Transparent_-_no_inhib_barrel2/1'>barrel 2</scene>) in the heavy chain. The greek key barrel is characterized as an up and down β-barrel with an n+3 linkage across the barrel, in this case, the across barrel linkage is an α-helix. The <scene name='Factor_Xa/Transparent_-no_inhib-_barrels/1'>two barrels</scene> pack together asymmetrically to constitute the compact <scene name='Factor_Xa/Transparent_-_barrels_catalyt/1'>catalytic domain</scene> (see below for more information). Although the hydrophobic core structures remain conserved throughout the family (12), considerable variation is seen in the surface loops, especially surrounding the active site where they determine substrate specificities. <ref>PMID: 9707558</ref> | The members of the trypsin-like serine protease family have two homologous greek key β-barrel subdomains (<scene name='Factor_Xa/Transparent_-no_inhib-_barrel1/1'>barrel 1</scene>, <scene name='Factor_Xa/Transparent_-_no_inhib_barrel2/1'>barrel 2</scene>) in the heavy chain. The greek key barrel is characterized as an up and down β-barrel with an n+3 linkage across the barrel, in this case, the across barrel linkage is an α-helix. The <scene name='Factor_Xa/Transparent_-no_inhib-_barrels/1'>two barrels</scene> pack together asymmetrically to constitute the compact <scene name='Factor_Xa/Transparent_-_barrels_catalyt/1'>catalytic domain</scene> (see below for more information). Although the hydrophobic core structures remain conserved throughout the family (12), considerable variation is seen in the surface loops, especially surrounding the active site where they determine substrate specificities. <ref>PMID: 9707558</ref> | ||
====Catalytic Triad==== | |||
Serine proteases use a His57, Asp102, Ser195 [http://en.wikipedia.org/wiki/Catalytic_triad catalytic triad], each playing an important role. The serine donates an OH group to act as a nucleophile and attack the carbonyl group of the peptide bond that will be broken within the substrate. Histidine coordinates the attack of the peptide bond by accepting the hydrogen from the serine –OH group with a pair of electrons on nitrogen. Aspartate contains a carboxyl group that aids in proper positioning of the histidine and stabilization, through hydrogen bonding. | |||
====Substrate Recognition Sites ==== | ====Substrate Recognition Sites ==== | ||
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The precise interactions of the P' side chains have not been defined. The P1' and P3' residues point in the same direction as a consequence of the beta sheet alignment of the substrate, so that the S1' and S3' sites overlap. The S1'/S3' sites are bounded by His57, the 60’s loop and the 40’s loop. The P2' residue points in the opposite direction and may interact with the 150’s loop. | The precise interactions of the P' side chains have not been defined. The P1' and P3' residues point in the same direction as a consequence of the beta sheet alignment of the substrate, so that the S1' and S3' sites overlap. The S1'/S3' sites are bounded by His57, the 60’s loop and the 40’s loop. The P2' residue points in the opposite direction and may interact with the 150’s loop. | ||
====Helix capping ==== | ====Helix capping ==== | ||
