Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

A single residue affects the dynamics and shape of a tetrameric GH43 β-1,4-d-xylosidase from Levilactobacillus brevis DSM1269

Linares-Pastén, Javier A. LU orcid ; Faryar, Reza LU ; Torrez Alvarez, Sergio LU ; Albasri, Khalil ; Shuoker, Bashar ; Abou Hachem, Maher LU ; Logan, Derek T. LU orcid and Karlsson, Eva Nordberg LU orcid (2025) In Protein Science 34(10). p.70299-70299
Abstract
Lignocellulosic materials (e.g., straw and bran) are gaining interest as feedstocks for the manufacture of higher value products, recognizing xylooligosaccharides (XOS) as interesting prebiotic compounds, and putting enzymes converting xylooligosaccharides into focus. In this work, we are investigating a XOS converting enzyme from the probiotic bacterium Levilactobacillus brevis (formerly Lactobacillus brevis). Growth of multiple L. brevis strains, recognized as probiotics, is promoted by the presence of XOS. This study elucidates the 3D structure of an intracellular L. brevis β-xylosidase, LbXyn43B from glycoside hydrolase family 43 (GH43), resolving it to 1.9 Å resolution. Functional analysis identified... (More)
Lignocellulosic materials (e.g., straw and bran) are gaining interest as feedstocks for the manufacture of higher value products, recognizing xylooligosaccharides (XOS) as interesting prebiotic compounds, and putting enzymes converting xylooligosaccharides into focus. In this work, we are investigating a XOS converting enzyme from the probiotic bacterium Levilactobacillus brevis (formerly Lactobacillus brevis). Growth of multiple L. brevis strains, recognized as probiotics, is promoted by the presence of XOS. This study elucidates the 3D structure of an intracellular L. brevis β-xylosidase, LbXyn43B from glycoside hydrolase family 43 (GH43), resolving it to 1.9 Å resolution. Functional analysis identified LbXyn43B as a mediator for XOS utilization in L. brevis DSM1269. The enzyme, featuring a 5-fold β-propeller fold typical of GH43, prefers short XOS substrates, notably β-1,4-xylobiose and β-1,4-xylotriose, aligning with its role in hydrolyzing internalized XOS. Intriguingly, crystallographic and size exclusion chromatographic evidence reveals LbXyn43B to be a tetramer, contrary to the dimeric structure previously reported in a closely related homolog from strain DSM20054. Despite sharing a high sequence identity (differing in only five residues), Thr274 in LbXyn43B within a subunit interface loop was found to influence the tetramer's shape. When mutated to Ala (the residue at the corresponding position in the homolog), the enzyme's apparent native molecular mass was impacted, resulting in a more compact oligomeric structure of slightly higher thermostability. Kinetic analysis and molecular dynamics simulations further suggest an effect of Thr274Ala substitution in modulating the accessibility of longer oligosaccharides, such as β-1,4-d-xylotetraose, to the active site. (Less)
Please use this url to cite or link to this publication:
author
; ; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Levilactobacillus brevis/enzymology, Xylosidases/chemistry, Bacterial Proteins/chemistry, Oligosaccharides/metabolism, Crystallography, X-Ray, Glucuronates/metabolism, Protein Multimerization
in
Protein Science
volume
34
issue
10
pages
19 pages
publisher
The Protein Society
external identifiers
  • pmid:40944464
  • scopus:105015409059
ISSN
1469-896X
DOI
10.1002/pro.70299
language
English
LU publication?
yes
additional info
© 2025 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.
id
001044c5-3bc9-4945-b0c2-c2baaa890f8d
date added to LUP
2025-09-18 15:11:44
date last changed
2025-10-22 04:01:32
@article{001044c5-3bc9-4945-b0c2-c2baaa890f8d,
  abstract     = {{Lignocellulosic materials (e.g., straw and bran) are gaining interest as feedstocks for the manufacture of higher value products, recognizing xylooligosaccharides (XOS) as interesting prebiotic compounds, and putting enzymes converting xylooligosaccharides into focus. In this work, we are investigating a XOS converting enzyme from the probiotic bacterium <i>Levilactobacillus brevis</i> (formerly <i>Lactobacillus brevis</i>). Growth of multiple <i>L. brevis</i> strains, recognized as probiotics, is promoted by the presence of XOS. This study elucidates the 3D structure of an intracellular <i>L. brevis</i> β-xylosidase, <i>Lb</i>Xyn43B from glycoside hydrolase family 43 (GH43), resolving it to 1.9 Å resolution. Functional analysis identified <i>Lb</i>Xyn43B as a mediator for XOS utilization in <i>L. brevis</i> DSM1269. The enzyme, featuring a 5-fold β-propeller fold typical of GH43, prefers short XOS substrates, notably β-1,4-xylobiose and β-1,4-xylotriose, aligning with its role in hydrolyzing internalized XOS. Intriguingly, crystallographic and size exclusion chromatographic evidence reveals <i>Lb</i>Xyn43B to be a tetramer, contrary to the dimeric structure previously reported in a closely related homolog from strain DSM20054. Despite sharing a high sequence identity (differing in only five residues), Thr274 in <i>Lb</i>Xyn43B within a subunit interface loop was found to influence the tetramer's shape. When mutated to Ala (the residue at the corresponding position in the homolog), the enzyme's apparent native molecular mass was impacted, resulting in a more compact oligomeric structure of slightly higher thermostability. Kinetic analysis and molecular dynamics simulations further suggest an effect of Thr274Ala substitution in modulating the accessibility of longer oligosaccharides, such as β-1,4-d-xylotetraose, to the active site.}},
  author       = {{Linares-Pastén, Javier A. and Faryar, Reza and Torrez Alvarez, Sergio and Albasri, Khalil and Shuoker, Bashar and Abou Hachem, Maher and Logan, Derek T. and Karlsson, Eva Nordberg}},
  issn         = {{1469-896X}},
  keywords     = {{Levilactobacillus brevis/enzymology; Xylosidases/chemistry; Bacterial Proteins/chemistry; Oligosaccharides/metabolism; Crystallography, X-Ray; Glucuronates/metabolism; Protein Multimerization}},
  language     = {{eng}},
  number       = {{10}},
  pages        = {{70299--70299}},
  publisher    = {{The Protein Society}},
  series       = {{Protein Science}},
  title        = {{A single residue affects the dynamics and shape of a tetrameric GH43 β-1,4-d-xylosidase from <i>Levilactobacillus brevis</i> DSM1269}},
  url          = {{http://dx.doi.org/10.1002/pro.70299}},
  doi          = {{10.1002/pro.70299}},
  volume       = {{34}},
  year         = {{2025}},
}