8RG3 | pdb_00008rg3

Crystal structure of PbFucA from Planctomycetes bacterium K23_9 in P 1 21 1

• PDB DOI: https://doi.org/10.2210/pdb8RG3/pdb

• Classification: HYDROLASE
• Organism(s): Stieleria marina
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-13 Released: 2025-01-01 
• Deposition Author(s): Perez-Curz, C., Moraleda-Montoya, A., Liebana, R., Lorizate, M., Arrizabalaga, U., Garcia-Alija, M., Terrones, O., Contreras, F.X., Guerin, M.E., Trastoy, B., Alonso-Saez, L.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.253 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: in silico

Literature

Mechanisms of recalcitrant fucoidan breakdown in marine Planctomycetota.

Perez-Cruz, C., Moraleda-Montoya, A., Liebana, R., Terrones, O., Arrizabalaga, U., Garcia-Alija, M., Lorizate, M., Martinez Gascuena, A., Garcia-Alvarez, I., Nieto-Garai, J.A., Olazar-Intxausti, J., Rodriguez-Colinas, B., Mann, E., Chiara, J.L., Contreras, F.X., Guerin, M.E., Trastoy, B., Alonso-Saez, L.

(2024) Nat Commun 15: 10906-10906

• PubMed: 39738071 
• DOI: https://doi.org/10.1038/s41467-024-55268-w
• Primary Citation of Related Structures:  
  8RG3, 8RG4, 8RG5, 9F9V


• PubMed Abstract: 
  

  Marine brown algae produce the highly recalcitrant polysaccharide fucoidan, contributing to long-term oceanic carbon storage and climate regulation. Fucoidan is degraded by specialized heterotrophic bacteria, which promote ecosystem function and global carbon turnover using largely uncharacterized mechanisms. Here, we isolate and study two Planctomycetota strains from the microbiome associated with the alga Fucus spiralis, which grow efficiently on chemically diverse fucoidans. One of the strains appears to internalize the polymer, while the other strain degrades it extracellularly. Multi-omic approaches show that fucoidan breakdown is mediated by the expression of divergent polysaccharide utilization loci, and endo-fucanases of family GH168 are strongly upregulated during fucoidan digestion. Enzymatic assays and structural biology studies reveal how GH168 endo-fucanases degrade various fucoidan cores from brown algae, assisted by auxiliary hydrolytic enzymes. Overall, our results provide insights into fucoidan processing mechanisms in macroalgal-associated bacteria.

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Organizational Affiliation: 
• AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain.
Structural Glycoimmunology Laboratory, Biobizkaia Health Research Institute, Barakaldo, Spain.
Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, Spain.
Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria, Pozuelo de Alarcón, Madrid, Spain.
Instituto de Química Orgánica General (IQOG-CSIC), Madrid, Spain.
Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, Spain. [e-mail].
Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain. [e-mail].
Ikerbasque, Basque Foundation for Science, Bilbao, Spain. [e-mail].
Structural Glycobiology Laboratory, Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona Science Park, Tower R, Barcelona, Spain. [e-mail].
Structural Glycoimmunology Laboratory, Biobizkaia Health Research Institute, Barakaldo, Spain. [e-mail].
Ikerbasque, Basque Foundation for Science, Bilbao, Spain. [e-mail].
AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 260.31 kDa 
• Atom Count: 16,917 
• Modeled Residue Count: 2,134 
• Deposited Residue Count: 2,238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein	A, B, C, D, E, F	373	Stieleria marina	Mutation(s): 0  Gene Names: K239x_02140
UniProt
Find proteins for A0A517NMB4 (Stieleria marina) Explore A0A517NMB4  Go to UniProtKB:  A0A517NMB4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth A], H [auth B], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.253 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.841	α = 90
b = 81.897	β = 95.49
c = 160.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Perez-Curz, C., Moraleda-Montoya, A., Liebana, R., Lorizate, M., Arrizabalaga, U., Garcia-Alija, M., Terrones, O., Contreras, F.X., Guerin, M.E., Trastoy, B., Alonso-Saez, L.

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Funding Organization	Location	Grant Number
Other government	Spain	--

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release
  
• Version 1.1: 2025-01-08
  Changes: Database references