9FHX | pdb_00009fhx

Bacteroides ovatus polysaccharide lyase family 38 (BoPL38) wild type in complex tetramannuronic acid at pH 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.219 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Swiss Army Knife of Alginate Metabolism: Mechanistic Analysis of a Mixed-Function Polysaccharide Lyase/Epimerase of the Human Gut Microbiota.

Tandrup, T.Rivas-Fernandez, J.P.Madsen, M.Ronne, M.E.B Petersen, A.Klau, L.J.Tondervik, A.Wilkens, C.Aachmann, F.L.Rovira, C.Svensson, B.

(2025) J Am Chem Soc 147: 23594-23607

  • DOI: https://doi.org/10.1021/jacs.5c03557
  • Primary Citation of Related Structures:  
    9FHT, 9FHU, 9FHV, 9FHW, 9FHX, 9FHY, 9FHZ, 9FI0, 9FI1, 9FI2, 9FI3, 9FI4, 9FI5, 9FI6

  • PubMed Abstract: 

    The alginate-degrading enzyme Bo PL38 of the human gut bacterium Bacteroides ovatus CP926 degrades all three polysaccharide structures found in alginate, a major constituent of brown macroalgae, making it a valuable tool for the selective production of alginate oligosaccharides with industrial and biotechnological potential. Despite its abundance, alginate's heterogeneous composition limits its full utilization. Modification by epimerases and lyases can help to overcome this limitation, but typically requires distinct enzymes for each polysaccharide structure. Here, we combined experimental and computational approaches to elucidate the catalytic machinery that enables Bo PL38 to act across all alginate structures. We resolved in crystallo complexes of Bo PL38 with alginate oligosaccharides, providing key insights into substrate binding. These structures informed QM/MM MD simulations, which uncovered distinct conformational and reaction pathways for mannuronate and guluronate conversion. The simulations identified different transition states, showing how a single active site architecture facilitates C5 proton abstraction at subsite +1 by Y298 and H243, enabling syn - and anti -β-elimination, respectively. A well-defined residue network mediates substrate recognition, and site-directed mutagenesis revealed that disruption of this network destabilizes the active site architecture. Notably, R292 plays a critical role in distorting the sugar at subsite +1 into a preactivated conformation while also stabilizing the active site tunnel through a salt bridge. Finally, NMR spectroscopy revealed that Bo PL38 also catalyzes mannuronate-to-guluronate epimerization, highlighting its multifunctionality. These findings provide molecular insight into how a single enzyme accommodates alginate's structural diversity and offer new opportunities for enzymatic polysaccharide engineering.


  • Organizational Affiliation
    • Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alginate lyase family protein
A, B, C, D
404Bacteroides ovatusMutation(s): 0 
Gene Names: F3B53_17925F3D71_22350
UniProt
Find proteins for A0A173Y4C9 (Bacteroides xylanisolvens)
Explore A0A173Y4C9 
Go to UniProtKB:  A0A173Y4C9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A173Y4C9
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid
E, F, G, H
4N/A
Glycosylation Resources
GlyTouCan:  G72539QT
GlyCosmos:  G72539QT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.219 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.327α = 90
b = 89.355β = 120.561
c = 146.509γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmarkDFF170746

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Database references