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.

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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
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article
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0.00

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article

Structural, dynamic, and evolutionary determinants of substrate binding in the tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxydans

Ricardo Cabrera, Pietro Roversi, Pablo Villalobos, Pablo Maturana
bioRxiv (Cold Spring Harbor Laboratory)
Microbial metabolism and enzyme function
article

Structural, dynamic, and evolutionary determinants of substrate binding in the tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxydans

Ricardo Cabrera, Pietro Roversi, Pablo Villalobos, Pablo Maturana
article en

Abstract

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.

bioRxiv (Cold Spring Harbor Laboratory)
Universidad de Santiago de Chile (CL), Institute of Agricultural Biology and Biotechnology (IT), University of Chile (CL)
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
Openalex Percentile: Top 81%
Microbial metabolism and enzyme function
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