Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1T

Carbone, Vincenzo; Reilly, Kerri; Sang, Carrie; Schofield, Linley R.; Kelly, William J.; Ronimus, Ron S.; Attwood, Graeme T.; Palevich, Nikola

doi:10.3390/biom15050720

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Open AccessFeature PaperArticle

Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1^T

by

Vincenzo Carbone

,

Kerri Reilly

,

Carrie Sang

,

Linley R. Schofield

,

William J. Kelly

,

Ron S. Ronimus

,

Graeme T. Attwood

and

Nikola Palevich

^*

AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand

^*

Author to whom correspondence should be addressed.

Biomolecules 2025, 15(5), 720; https://doi.org/10.3390/biom15050720

Submission received: 11 April 2025 / Revised: 8 May 2025 / Accepted: 12 May 2025 / Published: 14 May 2025

(This article belongs to the Topic Design, Synthesis and Biological Evaluation of Novel Small Molecules as Multi-target Enzyme Inhibitors)

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Abstract

Pectin is a dynamic and complex polysaccharide that forms a substantial proportion of the primary plant cell wall and middle lamella of forage ingested by grazing ruminants. Pectin methylesterases (PMEs) are enzymes that belongs to the carbohydrate esterase family 8 (CE8) and catalyze the demethylesterification of pectin, a key polysaccharide in cell walls. Here we present the crystal structure of the catalytic domain of PmeC5 that is associated with a gene from Butyrivibrio fibrisolvens D1^T that encodes a large secreted pectinesterase family protein (2089 aa) determined to a resolution of 1.33 Å. Protein in silico modelling of the secreted pectinesterase confirmed the presence of an additional pectate lyase (PL9) and adhesin-like domains. The structure of PmeC5 was the characteristic right-handed parallel β-helical topology and active site residues of Asp231, Asp253, and Arg326 typical of the enzyme class. PmeC5 is a large modular enzyme that is characteristic of rumen B. fibrisolvens megaplasmids and plays a central role in degrading plant cell wall components and releasing methanol in the rumen environment. Such secreted PMEs are significant contributors to plant fiber digestion and methane production, making them attractive targets for both methane mitigation strategies and livestock productivity enhancement.

Keywords: Pectin methylesterase; Butyrivibrio; rumen; pectin; methanol

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MDPI and ACS Style

Carbone, V.; Reilly, K.; Sang, C.; Schofield, L.R.; Kelly, W.J.; Ronimus, R.S.; Attwood, G.T.; Palevich, N. Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1^T. Biomolecules 2025, 15, 720. https://doi.org/10.3390/biom15050720

AMA Style

Carbone V, Reilly K, Sang C, Schofield LR, Kelly WJ, Ronimus RS, Attwood GT, Palevich N. Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1^T. Biomolecules. 2025; 15(5):720. https://doi.org/10.3390/biom15050720

Chicago/Turabian Style

Carbone, Vincenzo, Kerri Reilly, Carrie Sang, Linley R. Schofield, William J. Kelly, Ron S. Ronimus, Graeme T. Attwood, and Nikola Palevich. 2025. "Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1^T" Biomolecules 15, no. 5: 720. https://doi.org/10.3390/biom15050720

APA Style

Carbone, V., Reilly, K., Sang, C., Schofield, L. R., Kelly, W. J., Ronimus, R. S., Attwood, G. T., & Palevich, N. (2025). Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1^T. Biomolecules, 15(5), 720. https://doi.org/10.3390/biom15050720

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Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1^T

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