Sandbox Reserved 322: Difference between revisions

← Older edit Newer edit →

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA, Brian Huang, Eric Ginter

@@ Line 21: / Line 21: @@
 One site of the active-site cleft is partially defined by the central 8-stranded <scene name='Sandbox_Reserved_322/8-stranded_beta-sheet/1'>β-sheet</scene>, and the <scene name='Sandbox_Reserved_322/Metal_binding_sites/1'>metal binding sites</scene> is located on the edge of the β-sheet<ref name="d"/>. The metal ion that is more deeply situated in the active-site cleft is designated Mn<sup>2+</sup><sub>A</sub> while the other metal ion is designated Mn<sup>2+</sup><sub>B</sub>. Mn<sup>2+</sup><sub>A</sub> is coordinated by His 193, Asp 216, Asp 220, Asp 323 and a solvent molecule, with a square pyramidal geometry<ref name="b"/><ref name="d"/>. The solvent molecule bridges both metal ions and also donates a hydrogen bond to Asp 220<ref name="b"/><ref name="d"/>. Mn<sup>2+</sup><sub>B</sub> is coordinated by His 218, Asp 216, Asp 323, Asp 325 and the bridging solvent molecule in a distorted octahedral fashion<ref name="d"/>. All metal ligands except for Asp 220 make hydrogen-bond interactions with other protein residues, and these interactions contribute to the stability of the metal binding site<ref name="b"/><ref name="d"/>.
-There are three different types of bridging metal ligands that facilitate the observed spin coupling between Mn<sup>2+</sup><sub>A</sub> and Mn<sup>2+</sup><sub>B</sub><ref name="d"/>. For the first ligand, the carboxylate side chain of Asp 216 is a syn-syn bidentate bridging ligand, with Oδ1 coordinated to Mn<sup>2+</sup><sub>A</sub> and Oδ2 coordinated to Mn<sup>2+</sup><sub>B</sub><ref name="d"/>. For the second ligand, the carboxylate side chain of Asp 323 is a monodentate bridging ligand, with Oδ1 coordinated to both Mn<sup>2+</sup><sub>A</sub> and Mn<sup>2+</sup><sub>B</sub> with anti- and syn-coordination stereo-chemistry, respectively<ref name="d"/>. And finally the third ligand, is the solvent molecule bridges both manganese ion symmetrically<ref name="d"/>. Overall the two manganese metal role in arginase is to maintain proper function of the enzyme<ref name="b"/>. Also the Mn<sup>2+</sup> ions coordinate with water, orienting and stabilizing the molecule and allowing water to act as a nucleophile and attack L-arginine, hydrolyzing it into orinithine and urea<ref name="c"/>.
+There are three different types of bridging metal ligands that facilitate the observed spin coupling between Mn<sup>2+</sup><sub>A</sub> and Mn<sup>2+</sup><sub>B</sub><ref name="d"/>. For the first ligand, the carboxylate side chain of Asp 216 is a syn-syn bidentate bridging ligand, with Oδ1 coordinated to Mn<sup>2+</sup><sub>A</sub> and Oδ2 coordinated to Mn<sup>2+</sup><sub>B</sub><ref name="d"/>. For the second ligand, the carboxylate side chain of Asp 323 is a monodentate bridging ligand, with Oδ1 coordinated to both Mn<sup>2+</sup><sub>A</sub> and Mn<sup>2+</sup><sub>B</sub> with anti- and syn-coordination stereo-chemistry, respectively<ref name="b"/><ref name="d"/>. And finally the third ligand, is the solvent molecule bridges both manganese ion symmetrically<ref name="d"/>. Overall the two manganese metal role in arginase is to maintain proper function of the enzyme<ref name="b"/>. Also the Mn<sup>2+</sup> ions coordinate with water, orienting and stabilizing the molecule and allowing water to act as a nucleophile and attack L-arginine, hydrolyzing it into orinithine and urea<ref name="c"/>.
 ==='''Mechanism'''===
 ----
 [[Image:Mechanism_of_arginase.jpg]]
-In general arginase is known to convert L-arginine into urea and L-ornithine, via hydrolysis, the proposed mechanism is adopted from Kanyo and colleagues as shown in figure 3<ref name="d"/>. In the first step of the hydrolytic mechanism, Asp 220 stabilizes the metal-bridging hydroxide ion with a hydrogen bond during a nucleophilic attack at the guanidinium carbon of arginine<ref name="d"/>. The resulting tetrahedral intermediate fall apart once a proton is transferred to the amino group of ornithine, and the proton transfer is mediated by Asp 220<ref name="d"/>. It is proposed that His 233 shuttles a proton from bulk solvent to the ε-amino group of ornithine before production dissociation<ref name="d"/>. Before product dissociation, a water molecule displaces urea<ref name="d"/>. In addition, the metal coordination facilitates the ionization of this water molecule to regenerate a nucleophilic hydroxide ion<ref name="d"/>. Here, proton transfer to bulk solvent may again be mediated by shuttle-group His 233<ref name="d"/>.
+In general arginase is known to convert L-arginine into urea and L-ornithine, via hydrolysis, the proposed mechanism is adopted from Kanyo and colleagues as shown in figure 3<ref name="d"/>. In the first step of the hydrolytic mechanism, Asp 220 stabilizes the metal-bridging hydroxide ion with a hydrogen bond during a nucleophilic attack at the guanidinium carbon of arginine<ref name="b"/><ref name="d"/>. The resulting tetrahedral intermediate fall apart once a proton is transferred to the amino group of ornithine, and the proton transfer is mediated by Asp 220<ref name="b"/><ref name="d"/>. It is proposed that His 233 shuttles a proton from bulk solvent to the ε-amino group of ornithine before production dissociation<ref name="b"/><ref name="d"/>. Before product dissociation, a water molecule displaces urea<ref name="d"/>. In addition, the metal coordination facilitates the ionization of this water molecule to regenerate a nucleophilic hydroxide ion<ref name="d"/>. Here, proton transfer to bulk solvent may again be mediated by shuttle-group His 233<ref name="b"/><ref name="d"/>.
 ==='''Arginase and the Physiology of Sexual Arousal'''===
 ----