Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel

Mélanie Loiodice; Elodie Drula; Zak McIver; Svetlana Antonyuk; Arnaud Baslé; Marcelo Lima; Edwin A Yates; Dominic P Byrne; Jamie Coughlan; Andrew Leech; Shahram Mesdaghi; Daniel J Rigden; Sophie Drouillard; William Helbert; Bernard Henrissat; Nicolas Terrapon; Gareth S A Wright; Marie Couturier; Alan Cartmell

doi:10.1073/pnas.2421623122

Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel

Mélanie Loiodice, Elodie Drula, Zak McIver, Svetlana Antonyuk, Arnaud Baslé, Marcelo Lima, Edwin A Yates, Dominic P Byrne, Jamie Coughlan, Andrew Leech, Shahram Mesdaghi, Daniel J Rigden, Sophie Drouillard, William Helbert, Bernard Henrissat, Nicolas Terrapon, Gareth S A Wright, Marie Couturier, Alan Cartmell

Biology

Research output: Contribution to journal › Article › peer-review

Abstract

Acidic glycans are essential for the biology of multicellular eukaryotes. To utilize them, microbial life including symbionts and pathogens has evolved polysaccharide lyases (PL) that cleave their 1,4 glycosidic linkages via a β-elimination mechanism. PL family 33 (PL33) enzymes have the unusual ability to target a diverse range of glycosaminoglycans (GAGs), as well as the bacterial polymer, gellan gum. In order to gain more detailed insight into PL33 activities we recombinantly expressed 10 PL33 members derived from all major environments and further elucidated the detailed biochemical and biophysical properties of five, showing that their substrate specificity is conferred by variations in tunnel length and topography. The key amino acids involved in catalysis and substrate interactions were identified, and employing a combination of complementary biochemical, structural, and modeling approaches, we show that the tunnel topography is induced by substrate binding to the glycan. Structural and bioinformatic analyses revealed that these features are conserved across several lyase families as well as in mammalian GAG epimerases.

Original language	English
Article number	e2421623122
Number of pages	12
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	122
Issue number	7
DOIs	https://doi.org/10.1073/pnas.2421623122
Publication status	Published - 11 Feb 2025

Keywords

Polysaccharide-Lyases/metabolism
Substrate Specificity
Bacterial Proteins/metabolism
Bacteria/enzymology
Evolution, Molecular
Models, Molecular
Amino Acid Sequence
Binding Sites
Protein Binding
Polysaccharides/metabolism
Glycosaminoglycans/metabolism

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10.1073/pnas.2421623122Licence: CC BY

Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnelFinal published version, 5.23 MBLicence: CC BY

Cite this

Loiodice, M., Drula, E., McIver, Z., Antonyuk, S., Baslé, A., Lima, M., Yates, E. A., Byrne, D. P., Coughlan, J., Leech, A., Mesdaghi, S., Rigden, D. J., Drouillard, S., Helbert, W., Henrissat, B., Terrapon, N., Wright, G. S. A., Couturier, M., & Cartmell, A. (2025). Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel. Proceedings of the National Academy of Sciences of the United States of America, 122(7), Article e2421623122. https://doi.org/10.1073/pnas.2421623122

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title = "Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel",

abstract = "Acidic glycans are essential for the biology of multicellular eukaryotes. To utilize them, microbial life including symbionts and pathogens has evolved polysaccharide lyases (PL) that cleave their 1,4 glycosidic linkages via a β-elimination mechanism. PL family 33 (PL33) enzymes have the unusual ability to target a diverse range of glycosaminoglycans (GAGs), as well as the bacterial polymer, gellan gum. In order to gain more detailed insight into PL33 activities we recombinantly expressed 10 PL33 members derived from all major environments and further elucidated the detailed biochemical and biophysical properties of five, showing that their substrate specificity is conferred by variations in tunnel length and topography. The key amino acids involved in catalysis and substrate interactions were identified, and employing a combination of complementary biochemical, structural, and modeling approaches, we show that the tunnel topography is induced by substrate binding to the glycan. Structural and bioinformatic analyses revealed that these features are conserved across several lyase families as well as in mammalian GAG epimerases.",

keywords = "Polysaccharide-Lyases/metabolism, Substrate Specificity, Bacterial Proteins/metabolism, Bacteria/enzymology, Evolution, Molecular, Models, Molecular, Amino Acid Sequence, Binding Sites, Protein Binding, Polysaccharides/metabolism, Glycosaminoglycans/metabolism",

author = "M{\'e}lanie Loiodice and Elodie Drula and Zak McIver and Svetlana Antonyuk and Arnaud Basl{\'e} and Marcelo Lima and Yates, {Edwin A} and Byrne, {Dominic P} and Jamie Coughlan and Andrew Leech and Shahram Mesdaghi and Rigden, {Daniel J} and Sophie Drouillard and William Helbert and Bernard Henrissat and Nicolas Terrapon and Wright, {Gareth S A} and Marie Couturier and Alan Cartmell",

year = "2025",

month = feb,

day = "11",

doi = "10.1073/pnas.2421623122",

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Loiodice, M, Drula, E, McIver, Z, Antonyuk, S, Baslé, A, Lima, M, Yates, EA, Byrne, DP, Coughlan, J, Leech, A, Mesdaghi, S, Rigden, DJ, Drouillard, S, Helbert, W, Henrissat, B, Terrapon, N, Wright, GSA, Couturier, M & Cartmell, A 2025, 'Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel', Proceedings of the National Academy of Sciences of the United States of America, vol. 122, no. 7, e2421623122. https://doi.org/10.1073/pnas.2421623122

TY - JOUR

T1 - Bacterial polysaccharide lyase family 33

T2 - Specificity from an evolutionarily conserved binding tunnel

AU - Loiodice, Mélanie

AU - Drula, Elodie

AU - McIver, Zak

AU - Antonyuk, Svetlana

AU - Baslé, Arnaud

AU - Lima, Marcelo

AU - Yates, Edwin A

AU - Byrne, Dominic P

AU - Coughlan, Jamie

AU - Leech, Andrew

AU - Mesdaghi, Shahram

AU - Rigden, Daniel J

AU - Drouillard, Sophie

AU - Helbert, William

AU - Henrissat, Bernard

AU - Terrapon, Nicolas

AU - Wright, Gareth S A

AU - Couturier, Marie

AU - Cartmell, Alan

PY - 2025/2/11

Y1 - 2025/2/11

N2 - Acidic glycans are essential for the biology of multicellular eukaryotes. To utilize them, microbial life including symbionts and pathogens has evolved polysaccharide lyases (PL) that cleave their 1,4 glycosidic linkages via a β-elimination mechanism. PL family 33 (PL33) enzymes have the unusual ability to target a diverse range of glycosaminoglycans (GAGs), as well as the bacterial polymer, gellan gum. In order to gain more detailed insight into PL33 activities we recombinantly expressed 10 PL33 members derived from all major environments and further elucidated the detailed biochemical and biophysical properties of five, showing that their substrate specificity is conferred by variations in tunnel length and topography. The key amino acids involved in catalysis and substrate interactions were identified, and employing a combination of complementary biochemical, structural, and modeling approaches, we show that the tunnel topography is induced by substrate binding to the glycan. Structural and bioinformatic analyses revealed that these features are conserved across several lyase families as well as in mammalian GAG epimerases.

AB - Acidic glycans are essential for the biology of multicellular eukaryotes. To utilize them, microbial life including symbionts and pathogens has evolved polysaccharide lyases (PL) that cleave their 1,4 glycosidic linkages via a β-elimination mechanism. PL family 33 (PL33) enzymes have the unusual ability to target a diverse range of glycosaminoglycans (GAGs), as well as the bacterial polymer, gellan gum. In order to gain more detailed insight into PL33 activities we recombinantly expressed 10 PL33 members derived from all major environments and further elucidated the detailed biochemical and biophysical properties of five, showing that their substrate specificity is conferred by variations in tunnel length and topography. The key amino acids involved in catalysis and substrate interactions were identified, and employing a combination of complementary biochemical, structural, and modeling approaches, we show that the tunnel topography is induced by substrate binding to the glycan. Structural and bioinformatic analyses revealed that these features are conserved across several lyase families as well as in mammalian GAG epimerases.

KW - Polysaccharide-Lyases/metabolism

KW - Substrate Specificity

KW - Bacterial Proteins/metabolism

KW - Bacteria/enzymology

KW - Evolution, Molecular

KW - Models, Molecular

KW - Amino Acid Sequence

KW - Binding Sites

KW - Protein Binding

KW - Polysaccharides/metabolism

KW - Glycosaminoglycans/metabolism

U2 - 10.1073/pnas.2421623122

DO - 10.1073/pnas.2421623122

M3 - Article

C2 - 39932998

SN - 0027-8424

VL - 122

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 7

M1 - e2421623122

ER -