Graphics Gallery

Gale Rhodes
Chemistry Department
University of Southern Maine

Revised 2006/08/02

Learn how to use Swiss-PdbViewer. Work through sections 1-4 of the Swiss-PdbViewer Tutorial.

Topic: Fatty Acid Metabolism

Examples

A Tryglyceride

Click HERE to download a structural model of a tryglyceride/

  • Identify the glycerol portion of the molecule.
  • Identify the three fatty acids that are esterified to the glycerol.
  • Notice the conformations of the three fatty-acid chains. Why is one of them bent in the middle?
  • How would the bent fatty acid affect the melting point of this tryglyceride? Explain.

Medium-Chain Acyl-CoA Dehydrogenase

PDB files: 3MDD (enzyme and FAD) and 3MDE (enzyme, FAD, and octanoyl CoA substrate).

Compare these two models in the neighborhood of the FAD binding site. Click HERE for an SPV Project File with this view already set up.

  • Measure the distance from the carbon of octanoylCoA that donates hydride ion to FAD to the FAD atom that accepts the hydride. Use your text to be sure that you have the correct atoms. About how far must the hydrogen nucleus move in this hydride transfer?
  • Glutamic acid 376 is thought to be the general base that pulls off an alpha proton from the octanoyl substrate. Use SPV's torsion function (button farthest to the right on the Tool Bar) to find a Glu-76 side-chain conformation that comfortably reaches the substrate alpha carbon.
  • Both FAD and CoA contain AMP units. Do either of the AMPs bind in a typical nucleotide binding domain? (How do you spot this type of domain?)
  • Does the flavin mononucleotide of FAD bind in a nucleotide binding domain?

 

Methylmalonyl-coenzyme A mutase, complex with B-12

This enzyme catalyzes the final step in conversion of propionyl-CoA to succinyl-CoA. Propionyl-CoA is the end product of beta-oxidation of fatty acids contain odd numbers of carbons.

From the Protein Data Bank, download file 1REQ, a crystallgraphic model of the enzyme. This model contains bound glycerol in the active site, and also contains desulfo-coenzyme A, presumably in the site where it binds when providing the methylmalonyl group for conversion to succinyl-CoA. Finally, it contains cobalamin, but lacks the 5'-deoxyadenosyl group that is essential to generating a free radical purported to drive the rearrangement of methlymalonly-CoA to succinyl-CoA. The authors believe that cobalamin is in the reduced Co(II) state in this complex.

  • Select residues starting at 570 and ending at the C-terminus of chain A. Click ribn to display these residues as a ribbon model, and color the ribbon by secondary structure. Add the cobalamin (B12800, meaning B12, group #800) to the display as a stick model. What part of cobalamin protrudes into this C-terminal domain. Does the domain have a familiar conformation?
  • Compare the location of this part of the cobalamin structure (relative to the cobalt-containing, heme-like corrin ring system) to the location shown in your text. What might be the function of this part of the cobalamin structure when cobalamine is not bound to an enzyme?
  • What protein group replaces the ligand of the Mo (II) ion that is displaced by binding to this protein?
  • What atoms of glycerol correspond to what atoms of an appropriate substrate for this enzyme?

 

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