3WJ7

Crystal structure of gox2253

Summary for 3WJ7

• Entry DOI: 10.2210/pdb3wj7/pdb
• Descriptor: Putative oxidoreductase, MERCURY (II) ION (3 entities in total)
• Functional Keywords: sdr family protein, reductase, oxidoreductase
• Biological source: Gluconobacter oxydans
• Total number of polymer chains: 3
• Total formula weight: 112809.41

Authors

Yuan, Y.A.,Yin, B. (deposition date: 2013-10-05, release date: 2014-06-04, Last modification date: 2024-05-29)

Primary citation

Yin, B.,Cui, D.,Zhang, L.,Jiang, S.,Machida, S.,Yuan, Y.A.,Wei, D.
Structural insights into substrate and coenzyme preference by SDR family protein Gox2253 from Gluconobater oxydans.
Proteins, 82:2925-2935, 2014

PubMed Abstract: Gox2253 from Gluconobacter oxydans belongs to the short-chain dehydrogenases/reductases family, and catalyzes the reduction of heptanal, octanal, nonanal, and decanal with NADPH. To develop a robust working platform to engineer novel G. oxydans oxidoreductases with designed coenzyme preference, we adopted a structure based rational design strategy using computational predictions that considers the number of hydrogen bonds formed between enzyme and docked coenzyme. We report the crystal structure of Gox2253 at 2.6 Å resolution, ternary models of Gox2253 mutants in complex with NADH/short-chain aldehydes, and propose a structural mechanism of substrate selection. Molecular dynamics simulation shows that hydrogen bonds could form between 2'-hydroxyl group in the adenosine moiety of NADH and the side chain of Gox2253 mutant after arginine at position 42 is replaced with tyrosine or lysine. Consistent with the molecular dynamics prediction, Gox2253-R42Y/K mutants can use both NADH and NADPH as a coenzyme. Hence, the strategies here could provide a practical platform to engineer coenzyme selectivity for any given oxidoreductase and could serve as an additional consideration to engineer substrate-binding pockets.

PubMed: 24825769
DOI: 10.1002/prot.24603

Experimental method

X-RAY DIFFRACTION (2.6 Å)