Sandbox 42: Difference between revisions
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== Overview == | == Overview == | ||
The primary catalytic action of the enzyme lysozyme is to hydrolyze β(1→4) glycosidic linkages found in bacterial cell walls.<ref>http://lysozyme.co.uk/</ref> More specifically, lysozyme hydrolyzes the linkages from ''N''-acetylmuramic acid to ''N''-acetylglucosamine which occur in peptidoglycans of the cell wall. The small 14.3 kD Hen egg white lysozyme is one of the most widely studied lysozymes. | The primary catalytic action of the enzyme lysozyme is to hydrolyze β(1→4) glycosidic linkages found in bacterial cell walls.<ref>http://lysozyme.co.uk/</ref> More specifically, lysozyme hydrolyzes the linkages from ''N''-acetylmuramic acid to ''N''-acetylglucosamine which occur in peptidoglycans of the cell wall. The small 14.3 kD Hen egg white lysozyme is one of the most widely studied lysozymes.<ref>Voet, Voet, and Pratt. Fundamentals of Biochemistry. 3 ed. John Wiley & Sons: 2008.</ref> | ||
== Secondary structure == | == Secondary structure == | ||
Hen egg white lysozyme is formed from one polypetide chain 129 amino acids in length. Important <scene name='Sandbox_42/Secondary_structures/3'>secondary structures</scene> formed by the chain include 7 alpha helicies and 1 beta sheet consisting of 3 anti-parallel strands. 4 disulfide bonds are involved in folding of the chain. | Hen egg white lysozyme is formed from one polypetide chain 129 amino acids in length. Important <scene name='Sandbox_42/Secondary_structures/3'>secondary structures</scene> formed by the chain include 7 alpha helicies and 1 beta sheet consisting of 3 anti-parallel strands. 4 disulfide bonds are involved in folding of the chain. | ||
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== Active site and Binding == | == 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. A mutation of T4 lysozyme allows for | 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. | ||
== Comparative Structures == | == Comparative Structures == | ||
