9OOZ

Crystal structure of PqqT Y161W Variant with PQQ bound

Summary for 9OOZ

• Entry DOI: 10.2210/pdb9ooz/pdb
• Descriptor: ABC transporter substrate binding protein (Subunit A), PYRROLOQUINOLINE QUINONE, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: periplasmic binding protein, transport protein
• Biological source: Methylorubrum extorquens
• Total number of polymer chains: 1
• Total formula weight: 33321.79

Authors

Bruchs, A.T.,Thompson, P.J.,Nava-Matadamas, C.,Mohd, T.,Olshansky, L.,Bridwell-Rabb, J. (deposition date: 2025-05-16, release date: 2025-10-15, Last modification date: 2025-10-29)

Primary citation

Taher, M.,Thompson, P.J.,Nava-Matadamas, C.,Bruchs, A.T.,Bridwell-Rabb, J.,Olshansky, L.
Mechanistic Interrogation of a PQQ and Rare Earth-Dependent Artificial Metalloenzyme.
J.Am.Chem.Soc., 147:37104-37114, 2025

PubMed Abstract: Pyrroloquinoline quinone (PQQ)-binding proteins are found in diverse species and play key roles in the central metabolism of many methylotrophic bacteria, acting as redox-active cofactors in their alcohol dehydrogenase (ADH) enzymes. These enzymes also require a Lewis acidic metal ion to activate PQQ, and the 2011 discovery of lanthanide (Ln)-dependent ADH enzymes sparked a surge of interest in understanding their functional properties. However, key questions remain regarding the mechanism, metal ion-dependence, and electron transport processes of these enzymes. We report mechanistic, structural, and computational studies on an artificial metalloenzyme (ArM) containing a biomimetic active site that binds Ln, PQQ, and catalyzes benzyl alcohol dehydrogenation. These studies provide insights into the potential structure-function relationships present in natural MDHs. Examining the relative reactivities of substituted benzyl alcohol substrates revealed a kinetic isotope effect of 2.9 ± 0.4 and a linear free energy relationship consistent with one of the two mechanistic pathways widely proposed to operate in ADHs. Preparing ArMs with metal ions spanning the rare earth series, we observed decreasing reactivity with increasing Lewis acidity, a pattern consistent with that of natural ADH assays. In contrast to patterns observed in natural ADH assays, addition of ammonia had no effect on catalysis. Finally, investigating the role of a conserved active site residue through X-ray diffraction and molecular dynamics simulations, revealed a PQQ/substrate access channel critically regulated by this site. Together, these studies bear new insights into the mechanism, metal ion-dependence, and conformational dynamics associated with PQQ and rare earth-dependent enzymes.

PubMed: 41055952
DOI: 10.1021/jacs.5c08540

Experimental method

X-RAY DIFFRACTION (1.98 Å)