9QGZ

Crystal structure of a D-lactate dehydrogenase from Porcellio dilatatus

Summary for 9QGZ

• Entry DOI: 10.2210/pdb9qgz/pdb
• Descriptor: Glycolate oxidase, FLAVIN-ADENINE DINUCLEOTIDE, FE (III) ION, ... (4 entities in total)
• Functional Keywords: gut metagenome; oxidoreductases, lactate dehydrogenases, oxidoreductase
• Biological source: Porcellio dilatatus
• Total number of polymer chains: 8
• Total formula weight: 398493.34

Authors

Borges, P.T.,Frazao, C.,Martins, L.O. (deposition date: 2025-03-14, release date: 2025-12-03, Last modification date: 2026-01-14)

Primary citation

Coelho, C.,Taborda, A.,Lorena, C.,Frazao, T.,Verissimo, A.,Borges, P.T.,Brissos, V.,Tiago, I.,Martins, L.O.
Shotgun metagenomic mining reveals a new FAD-dependent D-lactate dehydrogenase in an isopod gut microbiome.
Appl.Environ.Microbiol., 91:e0148025-e0148025, 2025

PubMed Abstract: Shotgun metagenomic sequencing has emerged as a powerful tool for exploring microbial diversity and uncovering genes encoding novel biocatalysts from complex environments. Here, we report the discovery and characterization of a new FAD-dependent D-lactate dehydrogenase (PdG-D-LDH) from the gut microbiome of the isopod . The enzyme was identified through screening using BLAST and AlphaFold3 and functionally characterized as a homodimeric, thermoactive, and thermostable protein, demonstrating the robustness required for biotechnological applications. PdG-D-LDH exhibits a strong catalytic preference toward D-lactate and preferentially reduces quinones over cytochrome or molecular oxygen. X-ray crystallography revealed a VAO/PCMH-like fold with a solvent-accessible active site that harbors both a FAD cofactor and an Fe(II) ion. Molecular docking studies provided insights into the structural determinants of its stereoselective substrate recognition. Under mild conditions, the enzyme catalyzed the oxidation of D-lactate to pyruvate with a 90% yield after 24 h of reaction, using molecular oxygen as the electron acceptor.

PubMed: 41231970
DOI: 10.1128/aem.01480-25

Experimental method

X-RAY DIFFRACTION (2.84 Å)