8Z0X

Crystal structure of glyoxylate reductase from Acetobacter aceti in the apo form

Summary for 8Z0X

• Entry DOI: 10.2210/pdb8z0x/pdb
• Descriptor: 3-hydroxyisobutyrate dehydrogenase (2 entities in total)
• Functional Keywords: glyoxylate reductase apo form, oxidoreductase
• Biological source: Acetobacter aceti
• Total number of polymer chains: 8
• Total formula weight: 263918.53

Authors

Majumder, T.R.,Yoshizawa, T.,Inoue, M.,Aono, R.,Matsumura, H.,Mihara, H. (deposition date: 2024-04-10, release date: 2024-10-23, Last modification date: 2025-05-07)

Primary citation

Majumder, T.R.,Yoshizawa, T.,Inoue, M.,Aono, R.,Matsumura, H.,Mihara, H.
Structural insights into the mechanism underlying the dual cofactor specificity of glyoxylate reductase from Acetobacter aceti in the beta-hydroxyacid dehydrogenase family.
Biochim Biophys Acta Proteins Proteom, 1873:141051-141051, 2025

PubMed Abstract: The β-hydroxyacid dehydrogenase family exhibits diverse cofactor preferences: some enzymes favor NAD, others favor NADP, and a subset can utilize both NAD and NADPH. Glyoxylate reductase from Acetobacter aceti JCM 20276 (AacGR) exhibits a dual cofactor specificity for NADPH and NADH in its catalytic reduction of glyoxylate to glycolate. In contrast to conventional cofactor-discriminating motifs, NRX and DXX, found in NADP- and NAD-specific enzymes, respectively, AacGR has a TPS motif in the equivalent position. Here we report X-ray crystallographic analysis of AacGR in its ligand-free form, and in complexes with NADPH and NADH, revealing critical interactions: Ser41 of the TPS motif interacted with the 2'-phosphate group of NADPH, while no analogous interaction occurred with the ribose hydroxy groups of NADH. Moreover, the TPS motif resided within a characteristic β-turn-like structure adjacent to a long flexible loop. Site-directed mutagenesis and kinetic analyses suggest that Ser41 facilitates NADPH binding, while the lack of a direct interaction of the TPS motif with NADH may allow for NADH utilization. The conformational dynamics of the TPS-containing β-turn-like structure along with the flexible loop likely govern the dual cofactor specificity and catalytic turnover of AacGR.

PubMed: 39368682
DOI: 10.1016/j.bbapap.2024.141051

Experimental method

X-RAY DIFFRACTION (1.6 Å)