4H6R: Structure of Reduced Deinococcus Radiodurans Proline Dehydrogenase

Proline dehydrogenase (PRODH) catalyzes the FAD-dependent oxidation of proline to Delta(1)-pyrroline-5-carboxylate, which is the first step of proline catabolism. Here, we report the structures of proline dehydrogenase from Deinococcus radiodurans in the oxidized state complexed with the proline analogue l-tetrahydrofuroic acid and in the reduced state with the proline site vacant. The analogue binds against the si face of the FAD isoalloxazine and is protected from bulk solvent by helix alpha8 and the beta1-alpha1 loop. The FAD ribityl chain adopts two conformations in the E-S complex, which is unprecedented for flavoenzymes. One of the conformations is novel for the PRODH superfamily and may contribute to the low substrate affinity of Deinococcus PRODH. Reduction of the crystalline enzyme-inhibitor complex causes profound structural changes, including 20 degrees butterfly bending of the isoalloxazine, crankshaft rotation of the ribityl, shifting of alpha8 by 1.7 A, reconfiguration of the beta1-alpha1 loop, and rupture of the Arg291-Glu64 ion pair. These changes dramatically open the active site to facilitate product release and allow electron acceptors access to the reduced flavin. The structures suggest that the ion pair, which is conserved in the PRODH superfamily, functions as the active site gate. Mutagenesis of Glu64 to Ala decreases the catalytic efficiency 27-fold, which demonstrates the importance of the gate. Mutation of Gly63 decreases the efficiency 140-fold, which suggests that flexibility of the beta1-alpha1 loop is essential for optimal catalysis. The large conformational changes that are required to form the E-S complex suggest that conformational selection plays a role in substrate recognition.
PDB ID: 4H6RDownload
MMDB ID: 105646
PDB Deposition Date: 2012/9/19
Updated in MMDB: 2012/12 
Experimental Method:
x-ray diffraction
Resolution: 1.75  Å
Source Organism:
Similar Structures:
Biological Unit for 4H6R: monomeric; determined by author and by software (PISA)
Molecular Components in 4H6R
Label Count Molecule
Protein (1 molecule)
Proline Dehydrogenase(Gene symbol: DR_0814)
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

Citing MMDB