7W5N

The crystal structure of the reduced form of Gluconobacter oxydans WSH-004 SNDH

Summary for 7W5N

• Entry DOI: 10.2210/pdb7w5n/pdb
• Descriptor: L-sorbosone dehydrogenase, NAD(P) dependent, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (3 entities in total)
• Functional Keywords: l-sorbosone dehydrogenase, nad(p)+, oxidoreductase
• Biological source: Gluconobacter oxydans
• Total number of polymer chains: 4
• Total formula weight: 220797.68

Authors

Li, D.,Hou, X.D.,Rao, Y.J.,Yin, D.J.,Zhou, J.W.,Chen, J. (deposition date: 2021-11-30, release date: 2023-03-01, Last modification date: 2023-12-27)

Primary citation

Li, D.,Deng, Z.,Hou, X.,Qin, Z.,Wang, X.,Yin, D.,Chen, Y.,Rao, Y.,Chen, J.,Zhou, J.
Structural Insight into the Catalytic Mechanisms of an L-Sorbosone Dehydrogenase.
Adv Sci, 10:e2301955-e2301955, 2023

PubMed Abstract: L-Sorbosone dehydrogenase (SNDH) is a key enzyme involved in the biosynthesis of 2-keto-L-gulonic acid , which is a direct precursor for the industrial scale production of vitamin C. Elucidating the structure and the catalytic mechanism is essential for improving SNDH performance. By solving the crystal structures of SNDH from Gluconobacter oxydans WSH-004, a reversible disulfide bond between Cys295 and the catalytic Cys296 residues is discovered. It allowed SNDH to switch between oxidation and reduction states, resulting in opening or closing the substrate pocket. Moreover, the Cys296 is found to affect the NADP binding pose with SNDH. Combining the in vitro biochemical and site-directed mutagenesis studies, the redox-based dynamic regulation and the catalytic mechanisms of SNDH are proposed. Moreover, the mutants with enhanced activity are obtained by extending substrate channels. This study not only elucidates the physiological control mechanism of the dehydrogenase, but also provides a theoretical basis for engineering similar enzymes.

PubMed: 37679059
DOI: 10.1002/advs.202301955

Experimental method

X-RAY DIFFRACTION (2.988 Å)