8Y83

Crystal structure of a ketoreductase from Sphingobacterium siyangense SY1 with co-enzyme

Summary for 8Y83

• Entry DOI: 10.2210/pdb8y83/pdb
• Descriptor: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family), NICOTINAMIDE-ADENINE-DINUCLEOTIDE (3 entities in total)
• Functional Keywords: ssdr, catalysis, reaction, oxidoreductase
• Biological source: Sphingobacterium siyangense
• Total number of polymer chains: 2
• Total formula weight: 53219.77

Authors

Zheng, Z.R.,Wei, H.L.,Liu, W.D.,You, S. (deposition date: 2024-02-05, release date: 2024-06-12, Last modification date: 2024-12-25)

Primary citation

Che, C.,Zhang, W.,Xu, X.,Zheng, Z.,Wei, H.,Qin, B.,Jia, X.,Liu, W.,You, S.
Structure-based reshaping of a new ketoreductase from Sphingobacterium siyangense SY1 toward alpha-haloacetophenones.
Int.J.Biol.Macromol., 277:134157-134157, 2024

PubMed Abstract: Ketoreductases play an indispensable role in the asymmetric synthesis of chiral drug intermediates, and an in-depth understanding of their substrate selectivity can improve the efficiency of enzyme engineering. In this endeavor, a new short-chain dehydrogenase/reductase (SDR) SsSDR1 identified from Sphingobacterium siyangense SY1 by gene mining method was successfully cloned and functionally expressed in Escherichia coli. Its activity against halogenated acetophenones has been tested and the results illustrated that SsSDR1-WT exhibits high activity for 3,5-bis(trifluoromethyl)acetophenone (1f), an important precursor in the synthesis of aprepitant. In addition, SsSDR1-WT showed obvious substrate preference for acetophenones without α-halogen substitution compared to their α-halogen analogs. To explore the structural basis of substrate selectivity, the X-ray crystal structures of SsSDR1-WT in its apo form and the complex structure with NAD were resolved. Taking 2-chloro-1-(3, 4-difluorophenyl) ethanone (1i) as the representative α-haloacetophenone, the key sites affecting substrate selectivity of SsSDR1-WT were identified and through the rational remodeling of the cavities C1 and C2 of SsSDR1, an excellent mutant I144A/S153L with significantly improved activity against α-halogenated acetophenones was obtained. The asymmetric catalysis of 1f and 1i was performed at the scale of 50 mL, and the space-time yields (STY) of the two were 1200 and 6000 g/L∙d, respectively. This study not only provides valuable biocatalysts for halogenated acetophenones, but also yields insights into the relationship between the substrate-binding pocket and substrate selectivity.

PubMed: 39059522
DOI: 10.1016/j.ijbiomac.2024.134157

Experimental method

X-RAY DIFFRACTION (2 Å)