9SWG

Crystal structure of PpDyP E209A variant in complex with manganese

Summary for 9SWG

• Entry DOI: 10.2210/pdb9swg/pdb
• Descriptor: Dyp-type peroxidase family protein, PROTOPORPHYRIN IX CONTAINING FE, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: ppdyp-type peroxidase, manganese site, biocatalysis., oxidoreductase
• Biological source: Pseudomonas putida
• Total number of polymer chains: 6
• Total formula weight: 188678.25

Authors

Borges, P.T.,Lorena, C.,Martins, L.O. (deposition date: 2025-10-06, release date: 2026-10-21, Last modification date: 2026-10-28)

Primary citation

Rodrigues, C.F.,Lorena, C.,Frazao, T.,Brissos, V.,Borges, P.T.,Martins, L.O.
Heme-Proximal Loop Dynamics Modulate Mn(II) Oxidation in Pseudomonas putida MET94 DyP-type peroxidase.
J.Biol.Chem., :113622-113622, 2026

PubMed Abstract: Enzymatic Mn(II) oxidation is relevant to both natural lignin degradation and the development of new industrial biocatalysts. DyP-type peroxidases are versatile microbial biocatalysts with potential applications in lignocellulose valorization, but the structural features influencing their Mn(II)-oxidizing activity remain incompletely understood. We determined the X-ray crystal structure of PpDyP from Pseudomonas putida bound to Mn(II), identifying a heme-proximal Mn-binding environment defined by E135, E188, and E204 in loop regions surrounding the heme pocket. Mutagenesis and steady-state kinetics indicate that these residues cooperate to shape the Mn(II)-oxidation environment and support catalysis. We then examined the E209A variant, in which the non-coordinating residue E209, located near E204, was replaced by alanine. E209A increased apparent Mn(II)-oxidation turnover approximately fivefold. Structural analysis showed that E209A displaces E204 and rearranges Q203-mediated inter-loop contacts, supporting E204's structural contribution to organizing the heme-proximal loop environment. This rearrangement was associated with increased loop flexibility and greater heme exposure, supporting a more accessible and dynamically permissive heme-proximal architecture. A distal Mn(II)-binding site involving E237 and E240 was also observed in E209A, but mutational analysis suggests that it contributes mainly to residual activity when the heme-proximal site is perturbed. Finally, we show that Mn(II) oxidation by PpDyP markedly enhances the oxidation of lignin-relevant substrates, including 2,6-dimethoxyphenol, guaiacol, guaiacylglycerol-β-guaiacyl ether, and alkali lignin, by up to 100-fold. Together, these findings support loop-network modulation as a strategy to tune bacterial DyP peroxidases for lignin valorization and oxidative biotransformations.

PubMed: 42849735
DOI: 10.1016/j.jbc.2026.113622

Experimental method

X-RAY DIFFRACTION (3.21 Å)