PDB file 3MDE
This file depicts pig liver Medium Chain Acyl-CoA Dehydrogenase, co-crystallized with bound substrate octanyl-CoA. The structure was solved by J.-J.P. Kim, M. Wang, & R. Paschke in 1994.
Suggested display options:
Specific suggestions: Initially, make the protein
disappear by right clicking on the image and in the Select menu choose
Then select hetero-ligand, display as sticks and color CPK.
The protein is a dimer so there are two sets of ligands.
Identify FAD and octanyl-CoA (8-C fatty acid esterified to CoA).
Use the command line to select glu376, and display as ball & stick, with color CPK.
Glu376 abstracts H+, & FAD accepts a hydride, as a trans double bond forms between the a & b carbons (carbons #2 & 3) of the octanyl moiety of octanyl-CoA..
Where are the reactive groups of FAD and Glu376 located relative to carbons 2 & 3 of the octanyl moiety of octanyl-CoA?
How does the location of the reactive groups explain stereospecificity of the reaction?
Look for the interaction between the 2' OH of the ribityl moiety of FAD and the carbonyl oxygen of the thioester substrate.
Now make the protein reappear by selecting protein-protein and color
Try viewing with cartoon and spacefill displays.
Where is the substrate binding site relative to the enzyme surface?
Would you expect this enzyme to function as a monomer?
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