Pyruvate decarboxylase: Difference between revisions
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The <scene name='40/401493/Active_site/1'>active site</scene> of PDC consists of Glu 477, Asp28, His114, and His 115 as well as the thiamine diphosphate cofactor. Hydrogen bonding occurs between the substrate and Asp28, His114, and Thr73. In the catalytic step of the reaction mechanism, <scene name='Ken_Engle_SANDBOX/Glu_473/2'>Glu 473</scene>, shown in red, donates a proton to the pyruvate. The scene shows the close proximity of this residue to the pyruvate. The negative charge of the Glu residue following the protonation of the substrate leads to the destabilization of the pyruvate carboxylate group. Next the carboxyl group leaves, using thyiamine diphosphate as an electron sink (described below). Following decarboxylation in the final step of the mechanism, release of acetaldehyde, a proton is transferred to the Glu477 residue from a cofactor. After the protonation in a concerted step, a water molecule donates a proton to the substrate while receiving a proton from Glu477. As the proton is taken from the substrate, the electrons move to form a carbonyl, which leads to the release of the acetaldehyde | The <scene name='40/401493/Active_site/1'>active site</scene> of PDC consists of Glu 477, Asp28, His114, and His 115 as well as the thiamine diphosphate cofactor. Hydrogen bonding occurs between the substrate and Asp28, His114, and Thr73. In the catalytic step of the reaction mechanism, <scene name='Ken_Engle_SANDBOX/Glu_473/2'>Glu 473</scene>, shown in red, donates a proton to the pyruvate. The scene shows the close proximity of this residue to the pyruvate. The negative charge of the Glu residue following the protonation of the substrate leads to the destabilization of the pyruvate carboxylate group. Next the carboxyl group leaves, using thyiamine diphosphate as an electron sink (described below). Following decarboxylation in the final step of the mechanism, release of acetaldehyde, a proton is transferred to the Glu477 residue from a cofactor. After the protonation in a concerted step, a water molecule donates a proton to the substrate while receiving a proton from Glu477. As the proton is taken from the substrate, the electrons move to form a carbonyl, which leads to the release of the acetaldehyde. | ||
==Regulation== | ==Regulation== | ||
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*Pyruvate decarboxylase | *Pyruvate decarboxylase | ||
**[[ | **[[1zpd]], [[2wva]], [[2wvg]], [[2wvh]] - ZmPyD – ''Zymomonas mobilis''<br /> | ||
**[[2vk4]], [[6efg]] – KlPyD – ''Kluveromyces lactis''<br /> | **[[2vk4]], [[6efg]] – KlPyD – ''Kluveromyces lactis''<br /> | ||
**[[2vbi]] – PyD – ''Acetobacter pasteurianus''<br /> | **[[2vbi]] – PyD – ''Acetobacter pasteurianus''<br /> | ||
**[[3mve]] - VvPyD - ''Vibrio vulnificus''<br /> | **[[3mve]] - VvPyD - ''Vibrio vulnificus''<br /> | ||
**[[5euj]] - PyD - ''Zymobacter palmae''<br /> | **[[5euj]] - PyD - ''Zymobacter palmae''<br /> | ||
**[[8hp2]] - CtPyD – ''Candida tropicalis''<br /> | |||
*Pyruvate decarboxylase complex | *Pyruvate decarboxylase complex | ||
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**[[5npu]] - PyD + TPP - synthetic<br /> | **[[5npu]] - PyD + TPP - synthetic<br /> | ||
**[[3oe1]], [[4zp1]], [[5tma]] – ZmPyD (mutant) + ThDP derivative<br /> | **[[3oe1]], [[4zp1]], [[5tma]] – ZmPyD (mutant) + ThDP derivative<br /> | ||
**[[9s7j]] - PyD + ThDP – ''Neoasaia chiangmaiensis'' – Cryo EM<br /> | |||
**[[8hp4]] - CtPyD + ThDP<br /> | |||
}} | }} | ||
==Additional Resources== | ==Additional Resources== | ||
