Chemistry Department University of Southern Maine
Links To Files Used In Biochemistry Class (CHY 361-363)
Be sure to read the Introduction to the Biochemistry Graphics Gallery to learn how to view these files.
Topic: Fatty-Acid and Amino-Acid Catabolism
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Molecules to Explore
For views of some important cofactors studied in this section, obtain the following files from the Protein Data Bank.
Methylmalonyl-coenzyme A mutase, complex with B-12 (PDB file code 1REQ)
This enzyme catalyzes the final step in conversion of propionyl-CoA to succinyl-CoA. Propionyl is the end product of beta-oxidation of fatty acids contain odd numbers 2N of carbons C. The crystallgraphic model of this enzyme 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 lack 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.
Aspartate Aminotransferase, complex with PLP (PDB file codes 8AAT and 9AAT)
(Note: these are large files, and may take several minutes to download over a telephone modem.)
This enzyme catalyzes transaminase reactions involving oxaloacetate as nitrogen acceptor. The model in file 8AAT contains pyridoxal phosphate joined as an aldimine to the active-site lysine. The model in file 9AAT contains pyridoxamine in the active site.
Use SwissPdbViewer to compare these structures. They should be superimposed when loaded; if not, use Tools: Magic Fit to superimpose them. To examine cofactor binding, display groups within 5 angstroms Å of PLP, which is the last reside in chain A.
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