Structural, dynamic, and evolutionary determinants of substrate binding in the tetrameric 6-phosphogluconate dehydrogenase from <i>Gluconobacter oxydans</i>
6-Phosphogluconate dehydrogenases (6PGDHs) catalyze a key oxidative step in the oxidative pentose phosphate pathway (oxPPP), a route essential for NAD(P)H generation and carbon metabolism in bacteria and eukaryotes. While the structural basis of substrate recognition is well established for long-chain dimeric 6PGDHs, the mechanisms used by short-chain tetrameric enzymes remain poorly defined. Here, we present a 2.0 Å crystal structure of tetrameric 6PGDH from <i>Gluconobacter oxydans</i> (<i>Go</i>6PGDH) in complex with 6-phosphogluconate (6PG) and integrate it with evolutionary, computational, and functional analyses. The structure shows that, unlike dimeric homologs, tetrameric <i>Go</i>6PGDH does not undergo a domain-closure transition upon ligand binding. Instead, 6PG induces a compaction of the tetramer mediated by two conserved C-terminal elements: an inter-protomer ionic "lock" and an intra-subunit C-terminal "latch" that together stabilize a closed catalytic pocket. Molecular-dynamics simulations identify His328 as a central residue that couples C-terminal tail closure to direct ligand coordination, and mutagenesis analysis confirms its essential role in catalytic efficiency. Thermodynamic measurements reveal that 6PG binding is strongly enthalpy-driven, consistent with the formation of an ordered hydrogen-bonding and electrostatic network in the closed conformation. These findings define a substrate-induced quaternary-tightening mechanism unique to tetrameric 6PGDHs and illustrate how a conserved C-terminal module has been adapted across the family to regulate substrate binding and catalysis.
Authors
- Ricardo Cabrera (ORCID: https://orcid.org/0000-0002-8896-3172)
- Pietro Roversi (ORCID: https://orcid.org/0000-0001-9280-9437)
- Pablo Villalobos (ORCID: https://orcid.org/0000-0003-3207-332X)
- Pablo Maturana
Institutions
- Universidad de Santiago de Chile (CL)
- Institute of Agricultural Biology and Biotechnology (IT)
- University of Chile (CL)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-01-21
- DOI
- https://doi.org/10.64898/2026.01.21.700892
- Primary Topic
- Microbial metabolism and enzyme function
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- U.S. Department of Energy
- Office of Science
- Comisión Nacional de Investigación Científica y Tecnológica
- National Cancer Institute
- National Institute of General Medical Sciences
- Fondo Nacional de Desarrollo Científico y Tecnológico
- Argonne National Laboratory