8JB1

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 in complex with NADP

Summary for 8JB1

• Entry DOI: 10.2210/pdb8jb1/pdb
• Descriptor: Glyceraldehyde-3-phosphate dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, GLYCEROL, ... (4 entities in total)
• Functional Keywords: glycolysis, dehydrogenase, structural protein
• Biological source: Corynebacterium glutamicum ATCC 13032
• Total number of polymer chains: 2
• Total formula weight: 110445.33

Authors

Son, H.F.,Kim, K.J. (deposition date: 2023-05-07, release date: 2023-12-06)

Primary citation

Son, H.F.,Park, W.,Kim, S.,Kim, I.K.,Kim, K.J.
Structure-based functional analysis of a novel NADPH-producing glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum.
Int.J.Biol.Macromol., 255:128103-128103, 2023

PubMed Abstract: Corynebacterium glutamicum is an industrial workhorse applied in the production of valuable biochemicals. In the process of bio-based chemical production, improving cofactor recycling and mitigating cofactor imbalance are considered major solutions for enhancing the production yield and efficiency. Although, glyceraldehyde-3-phosphate dehydrogenase (GapDH), a glycolytic enzyme, can be a promising candidate for a sufficient NADPH cofactor supply, however, most microorganisms have only NAD-dependent GapDHs. In this study, we performed functional characterization and structure determination of novel NADPH-producing GapDH from C. glutamicum (CgGapX). Based on the crystal structure of CgGapX in complex with NADP cofactor, the unique structural features of CgGapX for NADP stabilization were elucidated. Also, N-terminal additional region (Auxiliary domain, AD) appears to have an effect on enzyme stabilization. In addition, through structure-guided enzyme engineering, we developed a CgGapX variant that exhibited 4.3-fold higher k, and 1.2-fold higher k/K values when compared with wild-type. Furthermore, a bioinformatic analysis of 100 GapX-like enzymes from 97 microorganisms in the KEGG database revealed that the GapX-like enzymes possess a variety of AD, which seem to determine enzyme stability. Our findings are expected to provide valuable information for supplying NADPH cofactor pools in bio-based value-added chemical production.

PubMed: 37992937
DOI: 10.1016/j.ijbiomac.2023.128103

Experimental method

X-RAY DIFFRACTION (2.44 Å)