7CFX

NAD-soaked Holo-methanol dehydrogenase (MDH) from Methylococcus capsulatus (Bath)

Summary for 7CFX

• Entry DOI: 10.2210/pdb7cfx/pdb
• Descriptor: Methanol dehydrogenase protein, large subunit, Methanol dehydrogenase [cytochrome c] subunit 2, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: nad, pqq, oxidoreductase
• Biological source: Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath); More
• Total number of polymer chains: 16
• Total formula weight: 578306.63

Authors

Chuankhayan, P.,Chan, S.I.,Nareddy, P.K.R.,Tsai, I.K.,Tsai, Y.F.,Chen, K.H.-C.,Yu, S.S.-F.,Chen, C.J. (deposition date: 2020-06-29, release date: 2021-06-30, Last modification date: 2024-10-23)

Primary citation

Chan, S.I.,Chuankhayan, P.,Reddy Nareddy, P.K.,Tsai, I.K.,Tsai, Y.F.,Chen, K.H.,Yu, S.S.,Chen, C.J.
Mechanism of Pyrroloquinoline Quinone-Dependent Hydride Transfer Chemistry from Spectroscopic and High-Resolution X-ray Structural Studies of the Methanol Dehydrogenase from Methylococcus capsulatus (Bath).
J.Am.Chem.Soc., 143:3359-3372, 2021

PubMed Abstract: The active site of methanol dehydrogenase (MDH) contains a rare disulfide bridge between adjacent cysteine residues. As a vicinal disulfide, the structure is highly strained, suggesting it might work together with the pyrroloquinoline quinone (PQQ) prosthetic group and the Ca ion in the catalytic turnover during methanol (CHOH) oxidation. We purify MDH from (Bath) with the disulfide bridge broken into two thiols. Spectroscopic and high-resolution X-ray crystallographic studies of this form of MDH indicate that the disulfide bridge is redox active. We observe an internal redox process within the -MDH that produces a disulfide radical anion concomitant with a companion PQQ radical, as evidenced by an optical absorption at 408 nm and a magnetically dipolar-coupled biradical in the EPR spectrum. These observations are corroborated by electron-density changes between the two cysteine sulfurs of the disulfide bridge as well as between the bound Ca ion and the O5-C5 bond of the PQQ in the high-resolution X-ray structure. On the basis of these findings, we propose a mechanism for the controlled redistribution of the two electrons during hydride transfer from the CHOH in the alcohol oxidation without formation of the reduced PQQ ethenediol, a biradical mechanism that allows for possible recovery of the hydride for transfer to an external NAD oxidant in the regeneration of the PQQ cofactor for multiple catalytic turnovers. In support of this mechanism, a steady-state level of the disulfide radical anion is observed during turnover of the MDH in the presence of CHOH and NAD.

PubMed: 33629832
DOI: 10.1021/jacs.0c11414

Experimental method

X-RAY DIFFRACTION (2.5 Å)