8HP0

Crystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis

Summary for 8HP0

• Entry DOI: 10.2210/pdb8hp0/pdb
• Descriptor: Meso-diaminopimelate D-dehydrogenase, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, SULFATE ION, ... (4 entities in total)
• Functional Keywords: asymmetric unit, c221, fold, oxidoreductase
• Biological source: Prevotella timonensis
• Total number of polymer chains: 3
• Total formula weight: 99236.86

Authors

Tan, Y.,Song, W. (deposition date: 2022-12-11, release date: 2023-12-13, Last modification date: 2024-02-21)

Primary citation

Tan, Y.,Gao, C.,Song, W.,Wei, W.,Liu, J.,Gao, C.,Guo, L.,Chen, X.,Liu, L.,Wu, J.
Rational Design of Meso -Diaminopimelate Dehydrogenase with Enhanced Reductive Amination Activity for Efficient Production of d- p -Hydroxyphenylglycine.
Appl.Environ.Microbiol., 89:e0010923-e0010923, 2023

PubMed Abstract: d--hydroxyphenylglycine (d-HPG) is an important intermediate in the pharmaceutical industry. In this study, a tri-enzyme cascade for the production of d-HPG from l-HPG was designed. However, the amination activity of Prevotella timonensis -diaminopimelate dehydrogenase (DAPDH) toward 4-hydroxyphenylglyoxylate (HPGA) was identified as the rate-limiting step. To overcome this issue, the crystal structure of DAPDH was solved, and a "binding pocket and conformation remodeling" strategy was developed to improve the catalytic activity toward HPGA. The best variant obtained, DAPDH, exhibited a catalytic efficiency (/) that was 26.75-fold higher than that of the wild type. This improvement was due to the enlarged substrate-binding pocket and enhanced hydrogen bond networks around the active center; meanwhile, the increased number of interdomain residue interactions drove the conformation distribution toward the closed state. Under optimal transformation conditions, DAPDH produced 19.8 g/L d-HPG from 40 g/L racemate DL-HPG in a 3 L fermenter within 10 h, with 49.5% conversion and >99% enantiomeric excess. Our study provides an efficient three-enzyme cascade pathway for the industrial production of d-HPG from racemate DL-HPG. d--hydroxyphenylglycine (d-HPG) is an important intermediate in the synthesis of antimicrobial compounds. d-HPG is mainly produced via chemical and enzymatic approaches, and enzymatic asymmetric amination employing diaminopimelate dehydrogenase (DAPDH) is considered an attractive method. However, the low catalytic activity of DAPDH toward bulky 2-keto acids limits its applications. In this study, we identified a DAPDH from Prevotella timonensis and created a mutant, DAPDH, which exhibited a catalytic efficiency (/) toward 4-hydroxyphenylglyoxylate that was 26.75-fold higher than that of the wild type. The novel strategy developed in this study has practical value for the production of d-HPG from inexpensive racemate DL-HPG.

PubMed: 37070978
DOI: 10.1128/aem.00109-23

Experimental method

X-RAY DIFFRACTION (2.47 Å)