Sandbox Reserved 1559: Difference between revisions

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== Structural highlights and structure-function relationships ==

This protein has a <scene name='82/823083/6ojttriad/1'>Catalytic Triad</scene> which consists of the amino acids Phe-59, Tyr101, and Lys-134. These amino acids play an important role in catalysis for the protein. Lys-134 proved to be the most important amino acid. The basic spacefill view of the entire protein allows for visualization of the different elements in different colors. The elements shown are carbon (Grey), nitrogen (Blue), and oxygen (Red). The <scene name='82/823083/Spacefill/1'>spacefill view</scene> also allows for visualization of different allosteric binding sites. This protein has a <scene name='82/823083/Nsl_ligand/1'>ligand</scene>, called NSL. The structural fold of LsdA is that of a <scene name='83/830391/Rainbow_7blade_beta_propeller/2'>seven-bladed β-propeller</scene>. The LsdA active site harbors a single Fe2+ ion that resides at the center of the β-propeller. This metal ion is coordinated in a tetragonal pyramidal fashion by four histidines (His-167, His-218, His-282, and His-472), this is called the <scene name='82/823083/Metal_binding_site/1'>metal-binding site</scene>. <scene name='82/823083/Hydrophobic/1'>Hydrophobic interactions</scene> are highlighted in grey, and polar regions are purple, while the ligand is yellow. This protein has a catalytic triad for binding that consists of tyrosine (hydrophilic), phenylalanine (hydrophobic), and lysine (has a positive charge).

This protein has a <scene name='82/823083/6ojttriad/1'>Catalytic Triad</scene> which consists of the amino acids Phe-59, Tyr101, and Lys-134. These amino acids play an important role in catalysis for the protein. Lys-134 proved to be the most important amino acid. The basic spacefill view of the entire protein allows for visualization of the different elements in different colors. The elements shown are carbon (Grey), nitrogen (Blue), and oxygen (Red). The <scene name='82/823083/Spacefill/1'>spacefill view</scene> also allows for visualization of different allosteric binding sites. This protein has a <scene name='82/823083/Nsl_ligand/1'>ligand</scene>, called NSL. The structural fold of LsdA is that of a <scene name='83/830391/Rainbow_7blade_beta_propeller/2'>seven-bladed β-propeller</scene>. <scene name='82/823083/Hydrophobic/1'>Hydrophobic interactions</scene> are highlighted in grey, and polar regions are purple, while the ligand is yellow. This protein has a catalytic triad for binding that consists of tyrosine (hydrophilic), phenylalanine (hydrophobic), and lysine (has a positive charge).

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The tertiary structure also creates a metal binding site of Histidines to keep the iron molecule in place. There have been two mechanisms proposed for Lsd's. In one mechanism, the hydroxystillbenoid is activated via the enzyme-catalyzed deprotonation of the 4-hydroxy group, which then allows electron delocalization toward an Fe3+. In the other mechanism, π electron density from the double bond is redistributed to the iron-oxy complex to form an Fe2+ cation intermediate. Deprotonation of the hydroxyl is demanding for both mechanisms and is assisted by Lys134 and Tyr101.

The tertiary structure also creates a <scene name='82/823083/Metal_binding_site/1'>metal-binding site</scene> of Histidines to keep the iron molecule in place. This site is located in the active site where the single Fe2+ ion resides at the center of the β-propeller. This metal ion is coordinated in a tetragonal pyramidal fashion by four histidines (His-167, His-218, His-282, and His-472). There have been two mechanisms proposed for Lsd's. In one mechanism, the hydroxystillbenoid is activated via the enzyme-catalyzed deprotonation of the 4-hydroxy group, which then allows electron delocalization toward an Fe3+. In the other mechanism, π electron density from the double bond is redistributed to the iron-oxy complex to form an Fe2+ cation intermediate. Deprotonation of the hydroxyl is demanding for both mechanisms and is assisted by Lys134 and Tyr101.

The hydrophobic/hydrophilic view of the ligand in the protein shows that both hydrophilic and hydrophobic residues are important to the ligand in the binding site. The first photo below shows the spacefill look at the protein, and it can be seen that the binding pocket is almost invisible and hard to reach. The second photo shows the hydrophobic/hydrophilic binding pocket up close, showing that the hydrophobic portion of the protein is interacting with the hydrophobic portion of the ligand, and the hydrophilic portion is interacting with the hydrophilic areas of the ligand. The red shows hydrophobic properties, and the green shows hydrophilic properties. In the first photo you can see on chain B the active site is mostly hydrophilic with one red hydrophobic area at the entrance. The ligand is in the middle of the protein and is not very visible from the outside of the protein.

Sandbox Reserved 1559: Difference between revisions

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@@ Line 13: / Line 13: @@
 == Structural highlights and structure-function relationships ==
-This protein has a  <scene name='82/823083/6ojttriad/1'>Catalytic Triad</scene> which consists of the amino acids Phe-59, Tyr101, and Lys-134. These amino acids play an important role in catalysis for the protein. Lys-134 proved to be the most important amino acid. The basic spacefill view of the entire protein allows for visualization of the different elements in different colors. The elements shown are carbon (Grey), nitrogen (Blue), and oxygen (Red). The <scene name='82/823083/Spacefill/1'>spacefill view</scene> also allows for visualization of different allosteric binding sites. This protein has a <scene name='82/823083/Nsl_ligand/1'>ligand</scene>, called NSL. The structural fold of LsdA is that of a  <scene name='83/830391/Rainbow_7blade_beta_propeller/2'>seven-bladed β-propeller</scene>. The LsdA active site harbors a single Fe2+ ion that resides at the center of the β-propeller. This metal ion is coordinated in a tetragonal pyramidal fashion by four histidines (His-167, His-218, His-282, and His-472), this is called the <scene name='82/823083/Metal_binding_site/1'>metal-binding site</scene>. <scene name='82/823083/Hydrophobic/1'>Hydrophobic interactions</scene> are highlighted in grey, and polar regions are purple, while the ligand is yellow. This protein has a catalytic triad for binding that consists of tyrosine (hydrophilic), phenylalanine (hydrophobic), and lysine (has a positive charge).
+This protein has a  <scene name='82/823083/6ojttriad/1'>Catalytic Triad</scene> which consists of the amino acids Phe-59, Tyr101, and Lys-134. These amino acids play an important role in catalysis for the protein. Lys-134 proved to be the most important amino acid. The basic spacefill view of the entire protein allows for visualization of the different elements in different colors. The elements shown are carbon (Grey), nitrogen (Blue), and oxygen (Red). The <scene name='82/823083/Spacefill/1'>spacefill view</scene> also allows for visualization of different allosteric binding sites. This protein has a <scene name='82/823083/Nsl_ligand/1'>ligand</scene>, called NSL. The structural fold of LsdA is that of a  <scene name='83/830391/Rainbow_7blade_beta_propeller/2'>seven-bladed β-propeller</scene>. <scene name='82/823083/Hydrophobic/1'>Hydrophobic interactions</scene> are highlighted in grey, and polar regions are purple, while the ligand is yellow. This protein has a catalytic triad for binding that consists of tyrosine (hydrophilic), phenylalanine (hydrophobic), and lysine (has a positive charge).
@@ Line 20: / Line 20: @@
-The tertiary structure also creates a metal binding site of Histidines to keep the iron molecule in place. There have been two mechanisms proposed for Lsd's. In one mechanism, the hydroxystillbenoid is activated via the enzyme-catalyzed deprotonation of the 4-hydroxy group, which then allows electron delocalization toward an Fe3+. In the other mechanism, π electron density from the double bond is redistributed to the iron-oxy complex to form an Fe2+ cation intermediate. Deprotonation of the hydroxyl is demanding for both mechanisms and is assisted by Lys134 and Tyr101.
+The tertiary structure also creates a <scene name='82/823083/Metal_binding_site/1'>metal-binding site</scene> of Histidines to keep the iron molecule in place. This site is located in the active site where the single Fe2+ ion resides at the center of the β-propeller. This metal ion is coordinated in a tetragonal pyramidal fashion by four histidines (His-167, His-218, His-282, and His-472). There have been two mechanisms proposed for Lsd's. In one mechanism, the hydroxystillbenoid is activated via the enzyme-catalyzed deprotonation of the 4-hydroxy group, which then allows electron delocalization toward an Fe3+. In the other mechanism, π electron density from the double bond is redistributed to the iron-oxy complex to form an Fe2+ cation intermediate. Deprotonation of the hydroxyl is demanding for both mechanisms and is assisted by Lys134 and Tyr101.
-The hydrophobic/hydrophilic view of the ligand in the protein shows that both hydrophilic and hydrophobic residues are important to the ligand in the binding site. The first photo below shows the spacefill look at the protein, and it can be seen that the binding pocket is almost invisible and hard to reach. The second photo shows the hydrophobic/hydrophilic binding pocket up close, showing that the hydrophobic portion of the protein is interacting with the hydrophobic portion of the ligand, and the hydrophilic portion is interacting with the hydrophilic areas of the ligand. The red shows hydrophobic properties, and the green shows hydrophilic properties. In the first photo you can see on chain B the active site is mostly hydrophilic with one red hydrophobic area at the entrance. The ligand is in the middle of the protein and is not very visible from the outside of the protein.