Pyruvate decarboxylase: Difference between revisions
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Thiamine diphosphate (ThDP) is an important cofactor in the pyruvate, acetaldehyde reaction. The <scene name='Ken_Engle_SANDBOX/Diphosphate_groups/2'>orange diphosphate group</scene> of this cofactor can be seen in this scene near the four active sites though they are hidden in other scenes by the ligand, pyruvate. ThDP actually binds the substrate during the first step of the reaction at C2 of the pyruvate. It is this ThDP that changes the environment of the active site which leads to the protonation or deprotonation of Glu473. When ThDP is not bound, the active site is not even open to bind pyruvate. When it binds, it causes a conformational change, moving Glu473 in such a way that forms a pocket for pyruvate’s methyl group<ref>PMID: 20099870 </ref>. | Thiamine diphosphate (ThDP) is an important cofactor in the pyruvate, acetaldehyde reaction. The <scene name='Ken_Engle_SANDBOX/Diphosphate_groups/2'>orange diphosphate group</scene> of this cofactor can be seen in this scene near the four active sites though they are hidden in other scenes by the ligand, pyruvate. ThDP actually binds the substrate during the first step of the reaction at C2 of the pyruvate. It is this ThDP that changes the environment of the active site which leads to the protonation or deprotonation of Glu473. When ThDP is not bound, the active site is not even open to bind pyruvate. When it binds, it causes a conformational change, moving Glu473 in such a way that forms a pocket for pyruvate’s methyl group<ref>PMID: 20099870 </ref>. | ||
==3D structures of pyruvate decarboxylase== | |||
===Pyruvate decarboxylase=== | |||
[[2wva]], [[2wvg]], [[2wvh]], [[1zpd]] - ZmPyD – Zymomonas mobilis<br /> | |||
[[2vk4]] – KlPyD – Kluveromyces lactis<br /> | |||
[[2vbi]] – PyD – Acetobacter pasteurianus | |||
===Pyruvate decarboxylase complex=== | |||
[[3oe1]] – ZmPyD (mutant) + lactyl-thiamin diphosphate<br /> | |||
[[2w93]] - yPyD (mutant) + pyruvamide – yeast<br /> | |||
[[1qpb]] - yPyD + pyruvamide<br /> | |||
[[1pvd]], [[1pyd]] - yPyD + thiamin diphosphate<br /> | |||
[[2vk1]] - yPyD (mutant) + pyruvic acid + thiamin diphosphate<br /> | |||
[[2vk8]] - yPyD (mutant) + hydroxypropanoic acid + thiamin diphosphate<br /> | |||
[[2vjy]] – KlPyD + substrate analog | |||
==Additional Resources== | ==Additional Resources== | ||