Sandbox 42: Difference between revisions

Line 12:

== Active site and Binding ==

Hen white lysozyme's substrate binding site accomodates six residue oligosaccharides. Glu 35 and Asp 52 are the enzyme's <scene name='Sandbox_42/Active_site/1'>active site residues</scene>. These residues have <scene name='Sandbox_42/Active_site_residue_contacts/1'>distinctly different microenvironments</scene> which are critical for their catalytic action. Asp 52 forms hydrogen bonds with surrounding residues including Asn46, Asp48, Ser50 and Asn59 on the anti-parallel beta-sheet and is negatively charged allowing for electrostatic stabilization of the reaction intermediate.<ref> PMID:19605465 </ref> Glu 35 conversely is surrounded by hydrophobic residues and its side chain stays protonated allowing for acid catalysis. Catalysis proceeds through the formation of a covalent intermediate.<ref>Voet, Voet, and Pratt. Fundamentals of Biochemistry. 3 ed. John Wiley & Sons: 2008.</ref> A mutation of T4 lysozyme allows for its product to stay bound to the enzyme. This mutation made it possible to isolate a <scene name='Sandbox_42/Ligand_and_lysozyme/1'>a covalent-substrate intermediate</scene> which also shows the predicted ~~distortion~~ of the sugar in the 4th position of the active site.

Hen white lysozyme's substrate binding site accomodates six residue oligosaccharides. Glu 35 and Asp 52 are the enzyme's <scene name='Sandbox_42/Active_site/1'>active site residues</scene>. These residues have <scene name='Sandbox_42/Active_site_residue_contacts/1'>distinctly different microenvironments</scene> which are critical for their catalytic action. Asp 52 forms hydrogen bonds with surrounding residues including Asn46, Asp48, Ser50 and Asn59 on the anti-parallel beta-sheet and is negatively charged allowing for electrostatic stabilization of the reaction intermediate.<ref> PMID:19605465 </ref> Glu 35 conversely is surrounded by hydrophobic residues and its side chain stays protonated allowing for acid catalysis. Catalysis proceeds through the formation of a covalent intermediate.<ref>Voet, Voet, and Pratt. Fundamentals of Biochemistry. 3 ed. John Wiley & Sons: 2008.</ref> A mutation of T4 lysozyme allows for its product to stay bound to the enzyme. This mutation made it possible to isolate a <scene name='Sandbox_42/Ligand_and_lysozyme/1'>a covalent-substrate intermediate</scene> which also shows the <scene name='Sandbox_42/Distorted_ring/1'>predicted distortio</scene>n of the sugar in the 4th position of the active site.

== Comparative Structures ==

Sandbox 42: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 12: / Line 12: @@
 == Active site and Binding ==
-Hen white lysozyme's substrate binding site accomodates six residue oligosaccharides. Glu 35 and Asp 52 are the enzyme's <scene name='Sandbox_42/Active_site/1'>active site residues</scene>. These residues have <scene name='Sandbox_42/Active_site_residue_contacts/1'>distinctly different microenvironments</scene> which are critical for their catalytic action. Asp 52 forms hydrogen bonds with surrounding residues including Asn46, Asp48, Ser50 and Asn59 on the anti-parallel beta-sheet and is negatively charged allowing for electrostatic stabilization of the reaction intermediate.<ref> PMID:19605465 </ref> Glu 35 conversely is surrounded by hydrophobic residues and its side chain stays protonated allowing for acid catalysis. Catalysis proceeds through the formation of a covalent intermediate.<ref>Voet, Voet, and Pratt. Fundamentals of Biochemistry. 3 ed. John Wiley & Sons: 2008.</ref> A mutation of T4 lysozyme allows for its product to stay bound to the enzyme. This mutation made it possible to isolate a <scene name='Sandbox_42/Ligand_and_lysozyme/1'>a covalent-substrate intermediate</scene> which also shows the predicted distortion of the sugar in the 4th position of the active site.
+Hen white lysozyme's substrate binding site accomodates six residue oligosaccharides. Glu 35 and Asp 52 are the enzyme's <scene name='Sandbox_42/Active_site/1'>active site residues</scene>. These residues have <scene name='Sandbox_42/Active_site_residue_contacts/1'>distinctly different microenvironments</scene> which are critical for their catalytic action. Asp 52 forms hydrogen bonds with surrounding residues including Asn46, Asp48, Ser50 and Asn59 on the anti-parallel beta-sheet and is negatively charged allowing for electrostatic stabilization of the reaction intermediate.<ref> PMID:19605465 </ref> Glu 35 conversely is surrounded by hydrophobic residues and its side chain stays protonated allowing for acid catalysis. Catalysis proceeds through the formation of a covalent intermediate.<ref>Voet, Voet, and Pratt. Fundamentals of Biochemistry. 3 ed. John Wiley & Sons: 2008.</ref> A mutation of T4 lysozyme allows for its product to stay bound to the enzyme. This mutation made it possible to isolate a <scene name='Sandbox_42/Ligand_and_lysozyme/1'>a covalent-substrate intermediate</scene> which also shows the <scene name='Sandbox_42/Distorted_ring/1'>predicted distortio</scene>n of the sugar in the 4th position of the active site.
 == Comparative Structures ==