8R43 | pdb_00008r43

Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant H110N in complex with tri-mannuronic acid

• PDB DOI: https://doi.org/10.2210/pdb8R43/pdb

• Classification: LYASE
• Organism(s): Paradendryphiella salina
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2023-11-12 Released: 2024-01-17 
• Deposition Author(s): Wilkens, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.87 Å
• R-Value Free: 
  0.141 (Depositor), 0.141 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Starting Model: experimental

Literature

Unraveling the molecular mechanism of polysaccharide lyases for efficient alginate degradation.

Rivas-Fernandez, J.P., Vuillemin, M., Pilgaard, B., Klau, L.J., Fredslund, F., Lund-Hanssen, C., Welner, D.H., Meyer, A.S., Morth, J.P., Meilleur, F., Aachmann, F.L., Rovira, C., Wilkens, C.

(2025) Nat Commun 16: 2670-2670

• PubMed: 40102416 
• DOI: https://doi.org/10.1038/s41467-025-56754-5
• Primary Citation Related Structures: 
  6YWF, 7NCZ, 7NL3, 7NM6, 7NPP, 7NY3, 7O6H, 7OOF, 7ORY, 7P25, 7P90, 7PBF, 8BJO, 8BXZ, 8C0M, 8C3X, 8P6O, 8PC3, 8PC8, 8PCX, 8PDT, 8PED, 8QIZ, 8QLI, 8QMJ, 8R43, 8RBI, 9G98, 9G99


• PubMed Abstract: 
  

  Alginate lyases (ALs) catalyze the depolymerization of brown macroalgae alginates, widely used naturally occurring polysaccharides. Their molecular reaction mechanism remains elusive due to the lack of catalytically competent Michaelis-Menten-like complex structures. Here, we provide structural snapshots and dissect the mechanism of mannuronan-specific ALs from family 7 polysaccharide lyases (PL7), employing time-resolved NMR, X-ray, neutron crystallography, and QM/MM simulations. We reveal the protonation state of critical active site residues, enabling atomic-level analysis of the reaction coordinate. Our approach reveals an endolytic and asynchronous syn β-elimination reaction, with Tyr serving as both Brønsted base and acid, involving a carbanion-type transition state. This study not only reconciles previous structural and kinetic discrepancies, but also establishes a comprehensive PL reaction mechanism which is most likely applicable across all enzymes of the PL7 family as well as other PL families.

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Organizational Affiliation: 
• Departament de Química Inorgànica i Orgànica (secció de Química Orgànica) & IQTCUB, Universitat de Barcelona, Barcelona, Spain.
Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Sciences, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
SINTEF Industry, Oslo, Norway.
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
Novo Nordisk A/S, Gentofte, Denmark.
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA.
Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Departament de Química Inorgànica i Orgànica (secció de Química Orgànica) & IQTCUB, Universitat de Barcelona, Barcelona, Spain. [e-mail].
Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, Barcelona, Spain. [e-mail].
Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. [e-mail].
Novo Nordisk Pharmatech A/S, Køge, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.09 kDa 
• Atom Count: 2,441 
• Modeled Residue Count: 228 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate lyase	A	234	Paradendryphiella salina	Mutation(s): 1  Gene Names: PsAlg7C
UniProt
Find proteins for A0A7I9C8Z1 (Paradendryphiella salina) Explore A0A7I9C8Z1  Go to UniProtKB:  A0A7I9C8Z1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid	B	3		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.87 Å
• R-Value Free:  0.141 (Depositor), 0.141 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.120 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.06	α = 90
b = 38.62	β = 116.76
c = 74.63	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Wilkens, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Database references, Structure summary