2ekg | pdb_00002ekg

Structure of Thermus thermophilus Proline Dehydrogenase inactivated by N-propargylglycine

spinqualitylabelsall models 2ekg, resolution 1.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2ekg is a 2 chain structure with sequence from Thet2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: FAD, MPD NonStd Res: LYX Related: 2g37 Gene: PROLINE DEHYDROGENASE/DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE (THET2) Activity: Proline dehydrogenase, with EC number 1.5.99.8 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. Structural basis for the inactivation of Thermus thermophilus proline dehydrogenase by N-propargylglycine.,White TA, Johnson WH Jr, Whitman CP, Tanner JJ Biochemistry. 2008 May 20;47(20):5573-80. Epub 2008 Apr 22. PMID:18426222 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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