9WXB

Cryo-EM structure of reduced form of formatedehydrogenase from Rhodobacter aestuarii (RaFDH) with NADH

Replaces:  9KTLReplaces:  9KTR

Summary for 9WXB

• Entry DOI: 10.2210/pdb9wxb/pdb
• Related: 9KTL 9KTR
• EMDB information: 66342
• Descriptor: Formate dehydrogenase delta subunit, FLAVIN MONONUCLEOTIDE, Formate dehydrogenase gamma subunit, ... (10 entities in total)
• Functional Keywords: formate dehydrogenase, formate oxidation, carbon dioxide redcution, fmn, nad, oxidoreductase
• Biological source: Rhodobacter aestuarii; More
• Total number of polymer chains: 8
• Total formula weight: 376022.81

Authors

Zhang, K.,Zhang, L. (deposition date: 2025-09-25, release date: 2026-06-03)

Primary citation

Zhang, K.,Liu, W.,Su, H.,Cui, H.,Wang, Y.,Zhu, Z.,You, C.,Zhang, L.
Understanding the Catalytic Determinant role of Diaphorase-Like Subunit in Formate Dehydrogenases via Redox Couples.
Adv Sci, :e75764-e75764, 2026

PubMed Abstract: Multi-subunit formate dehydrogenases (FDHs), which catalyze the interconversion of formate and carbon dioxide (CO), have drawn increasing attention for mitigating climate change and advancing environmental protection owing to their advantages of oxygen tolerance and easy heterogenous expression. However, differently sourced multi-subunit FDHs exhibit distinct catalytic biases, and the reasons remain unclear. On the basis of the exceptional observation of Rhodobacter aestuarii FDH favoring CO reduction, this study unveiled an oxidation inhibition effect in exclusively NADH/NAD-involved catalysis via kinetics analysis in terms of different redox couples. Substrate truncation positioned Fdhβ as the predominant subunit. Further studies based on structural and electrochemical insights interpreted that the slow desorption of NADH is the underlying determinant for the apparent catalytic bias. Knowledge-based rational design helped obtain a beneficial variant, RaFDH β E260Y, with a 10-fold increased catalytic activity in CO reduction, highlighting its potential for CO biotransformation and applications in low-carbon biomanufacturing. Eventually, bioinformatic analysis suggested that the diaphorase-like subunits and the catalysis regulation mechanism may widely exist in living organisms for modulating the redox balance of oxidoreductases, providing new insights into metabolism and catabolism.

PubMed: 42154453
DOI: 10.1002/advs.75764

Experimental method

ELECTRON MICROSCOPY (2.9 Å)