Group:SMART:2010 Pingry SMART Team: Difference between revisions

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The residues, <scene name='2010_Pingry_SMART_Team/1a80-original/17'>Ala47 and Trp77</scene>, are also found in all AKR enzymes in the active-site pocket. The active site pocket of 2,5 DKGR A is significantly smaller than the active-site pocket of human aldose reductase. The bottom of the pocket is made up of residues Phe22, Asp45, Ala47, Tyr50 (mentioned above), Lys75, Leu106, Ser139, Asn140, Trp187. The top rim of the pocket is formed by non-aromatic and apolar residues Ile49, Trp77, His108, and Trp109. The C-terminal is made up of residues Ser271 to Asp278. Ala47 and Trp77 are the only residues that are conserved in all AKR’s out of all of the active site residues. The C-terminus residues are involved in the formation of hydrogen bonds with the carbohydrate substrate as well as controlling the entry and alignment of the substrate in the active site.

Located on an extended conformation from the outer edge of the barrel is the binding site on 2,5-DKGR A for the <scene name='2010_Pingry_SMART_Team/1a80-original/12'>NADPH cofactor(shown in wireframe and colored CPK)</scene>. The NADPH cofactor is stabilized through hydrogen bonds, ionic bonds, and an aromatic pi-stacking interaction between <scene name='2010_Pingry_SMART_Team/1a80-original/19'>Trp187</scene> and the nicotinamide ring of NADPH. Although 2,5-DKGR A functions with NADPH as a cofactor, NADH is preferred for a more efficient production of vitamin C. To achieve this, mutations of the original side chains of Lys232, Phe22, Arg238, and Ala272 were conducted. Significantly, the <scene name='2010_Pingry_SMART_Team/1a80-default/1'>Lys232, Phe22, Arg238, and Ala272</scene> side chain interact with the phosphate group of NADPH. In order to accommodate for the cofactor, NADH, and the absent phosphate group, these side chains have been modified in the mutant form.

Located on an extended conformation from the outer edge of the barrel is the binding site on 2,5-DKGR A for the <scene name='2010_Pingry_SMART_Team/1a80-original/12'>NADPH cofactor(shown in wireframe and colored CPK)</scene>. The NADPH cofactor is stabilized through hydrogen bonds, ionic bonds, and an aromatic pi-stacking interaction between <scene name='2010_Pingry_SMART_Team/1a80-original/20'>Trp187</scene> and the nicotinamide ring of NADPH. Although 2,5-DKGR A functions with NADPH as a cofactor, NADH is preferred for a more efficient production of vitamin C. To achieve this, mutations of the original side chains of Lys232, Phe22, Arg238, and Ala272 were conducted. Significantly, the <scene name='2010_Pingry_SMART_Team/1a80-default/1'>Lys232, Phe22, Arg238, and Ala272</scene> side chain interact with the phosphate group of NADPH. In order to accommodate for the cofactor, NADH, and the absent phosphate group, these side chains have been modified in the mutant form.

Revision as of 23:34, 8 February 2010 view source Caryn Ha (talk \| contribs) 72 edits →‎PDB ID: 1a80, 2,5-diketo-d-gluconic acid reductase with NADPH (wild-type) ← Older edit		Revision as of 23:37, 8 February 2010 view source Caryn Ha (talk \| contribs) 72 edits →‎PDB ID: 1a80, 2,5-diketo-d-gluconic acid reductase with NADPH (wild-type) Newer edit →
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	The residues, <scene name='2010_Pingry_SMART_Team/1a80-original/17'>Ala47 and Trp77</scene>, are also found in all AKR enzymes in the active-site pocket. The active site pocket of 2,5 DKGR A is significantly smaller than the active-site pocket of human aldose reductase. The bottom of the pocket is made up of residues Phe22, Asp45, Ala47, Tyr50 (mentioned above), Lys75, Leu106, Ser139, Asn140, Trp187. The top rim of the pocket is formed by non-aromatic and apolar residues Ile49, Trp77, His108, and Trp109. The C-terminal is made up of residues Ser271 to Asp278. Ala47 and Trp77 are the only residues that are conserved in all AKR’s out of all of the active site residues. The C-terminus residues are involved in the formation of hydrogen bonds with the carbohydrate substrate as well as controlling the entry and alignment of the substrate in the active site.		The residues, <scene name='2010_Pingry_SMART_Team/1a80-original/17'>Ala47 and Trp77</scene>, are also found in all AKR enzymes in the active-site pocket. The active site pocket of 2,5 DKGR A is significantly smaller than the active-site pocket of human aldose reductase. The bottom of the pocket is made up of residues Phe22, Asp45, Ala47, Tyr50 (mentioned above), Lys75, Leu106, Ser139, Asn140, Trp187. The top rim of the pocket is formed by non-aromatic and apolar residues Ile49, Trp77, His108, and Trp109. The C-terminal is made up of residues Ser271 to Asp278. Ala47 and Trp77 are the only residues that are conserved in all AKR’s out of all of the active site residues. The C-terminus residues are involved in the formation of hydrogen bonds with the carbohydrate substrate as well as controlling the entry and alignment of the substrate in the active site.

	Located on an extended conformation from the outer edge of the barrel is the binding site on 2,5-DKGR A for the <scene name='2010_Pingry_SMART_Team/1a80-original/12'>NADPH cofactor(shown in wireframe and colored CPK)</scene>. The NADPH cofactor is stabilized through hydrogen bonds, ionic bonds, and an aromatic pi-stacking interaction between <scene name='2010_Pingry_SMART_Team/1a80-original/19'>Trp187</scene> and the nicotinamide ring of NADPH. Although 2,5-DKGR A functions with NADPH as a cofactor, NADH is preferred for a more efficient production of vitamin C. To achieve this, mutations of the original side chains of Lys232, Phe22, Arg238, and Ala272 were conducted. Significantly, the <scene name='2010_Pingry_SMART_Team/1a80-default/1'>Lys232, Phe22, Arg238, and Ala272</scene> side chain interact with the phosphate group of NADPH. In order to accommodate for the cofactor, NADH, and the absent phosphate group, these side chains have been modified in the mutant form.		Located on an extended conformation from the outer edge of the barrel is the binding site on 2,5-DKGR A for the <scene name='2010_Pingry_SMART_Team/1a80-original/12'>NADPH cofactor(shown in wireframe and colored CPK)</scene>. The NADPH cofactor is stabilized through hydrogen bonds, ionic bonds, and an aromatic pi-stacking interaction between <scene name='2010_Pingry_SMART_Team/1a80-original/20'>Trp187</scene> and the nicotinamide ring of NADPH. Although 2,5-DKGR A functions with NADPH as a cofactor, NADH is preferred for a more efficient production of vitamin C. To achieve this, mutations of the original side chains of Lys232, Phe22, Arg238, and Ala272 were conducted. Significantly, the <scene name='2010_Pingry_SMART_Team/1a80-default/1'>Lys232, Phe22, Arg238, and Ala272</scene> side chain interact with the phosphate group of NADPH. In order to accommodate for the cofactor, NADH, and the absent phosphate group, these side chains have been modified in the mutant form.