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 hide.
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 chain.
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?

Return to Lecture Notes
on Lipid Catabolism

Or press Back button
at top

to return to your place in the notes.