2EKG

Structure of Thermus thermophilus Proline Dehydrogenase inactivated by N-propargylglycine

Summary for 2EKG

• Entry DOI: 10.2210/pdb2ekg/pdb
• Related: 2g37
• Descriptor: Proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, FLAVIN-ADENINE DINUCLEOTIDE, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total)
• Functional Keywords: proline dehydrogenase, flavoenzyme, prodh, beta-alpha-barrel, suicide inhibitor, inactivation, flavocyanine, oxidoreductase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 2
• Total formula weight: 79776.63

Authors

White, T.A.,Tanner, J.J. (deposition date: 2007-03-23, release date: 2008-04-01, Last modification date: 2023-10-25)

Primary citation

White, T.A.,Johnson, W.H.,Whitman, C.P.,Tanner, J.J.
Structural basis for the inactivation of Thermus thermophilus proline dehydrogenase by N-propargylglycine
Biochemistry, 47:5573-5580, 2008

PubMed Abstract: The flavoenzyme proline dehydrogenase catalyzes the first step of proline catabolism, the oxidation of proline to pyrroline-5-carboxylate. Here we report the first crystal structure of an irreversibly inactivated proline dehydrogenase. The 1.9 A resolution structure of Thermus thermophilus proline dehydrogenase inactivated by the mechanism-based inhibitor N-propargylglycine shows that N5 of the flavin cofactor is covalently connected to the -amino group of Lys99 via a three-carbon linkage, consistent with the mass spectral analysis of the inactivated enzyme. The isoalloxazine ring has a butterfly angle of 25 degrees , which suggests that the flavin cofactor is reduced. Two mechanisms can account for these observations. In both, N-propargylglycine is oxidized to N-propargyliminoglycine. In one mechanism, this alpha,beta-unsaturated iminium compound is attacked by the N5 atom of the now reduced flavin to produce a 1,4-addition product. Schiff base formation between Lys99 and the imine of the 1,4-addition product releases glycine and links the enzyme to the modified flavin. In the second mechanism, hydrolysis of N-propargyliminoglycine yields propynal and glycine. A 1,4-addition reaction with propynal coupled with Schiff base formation between Lys99 and the carbonyl group tethers the enzyme to the flavin via a three-carbon chain. The presumed nonenzymatic hydrolysis of N-propargyliminoglycine and the subsequent rebinding of propynal to the enzyme make the latter mechanism less likely.

PubMed: 18426222
DOI: 10.1021/bi800055w

Experimental method

X-RAY DIFFRACTION (1.9 Å)