7ZO0 | pdb_00007zo0

Crystal structure of catalytic inactive unliganded form of FucOB, a GH95 family alpha-1,2-fucosidase from Akkermansia muciniphila

• PDB DOI: https://doi.org/10.2210/pdb7ZO0/pdb

• Classification: HYDROLASE
• Organism(s): Akkermansia muciniphila ATCC BAA-835
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-04-23 Released: 2023-04-19 
• Deposition Author(s): Anso, I., Cifuente, J.O., Trastoy, B., Guerin, M.E.
• Funding Organization(s): Ministry of Economy and Competitiveness (MINECO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Turning universal O into rare Bombay type blood.

Anso, I., Naegeli, A., Cifuente, J.O., Orrantia, A., Andersson, E., Zenarruzabeitia, O., Moraleda-Montoya, A., Garcia-Alija, M., Corzana, F., Del Orbe, R.A., Borrego, F., Trastoy, B., Sjogren, J., Guerin, M.E.

(2023) Nat Commun 14: 1765-1765

• PubMed: 36997505 
• DOI: https://doi.org/10.1038/s41467-023-37324-z
• Primary Citation Related Structures: 
  7ZNZ, 7ZO0


• PubMed Abstract: 
  

  Red blood cell antigens play critical roles in blood transfusion since donor incompatibilities can be lethal. Recipients with the rare total deficiency in H antigen, the O _h Bombay phenotype, can only be transfused with group O _h blood to avoid serious transfusion reactions. We discover FucOB from the mucin-degrading bacteria Akkermansia muciniphila as an α-1,2-fucosidase able to hydrolyze Type I, Type II, Type III and Type V H antigens to obtain the afucosylated Bombay phenotype in vitro. X-ray crystal structures of FucOB show a three-domain architecture, including a GH95 glycoside hydrolase. The structural data together with site-directed mutagenesis, enzymatic activity and computational methods provide molecular insights into substrate specificity and catalysis. Furthermore, using agglutination tests and flow cytometry-based techniques, we demonstrate the ability of FucOB to convert universal O type into rare Bombay type blood, providing exciting possibilities to facilitate transfusion in recipients/patients with Bombay phenotype.

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Organizational Affiliation: 
• Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903, Barakaldo, Bizkaia, Spain.
Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
Genovis AB, Box 790, 22007, Lund, Sweden.
Immunopathology Group, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903, Barakaldo, Bizkaia, Spain.
Departamento Química and Centro de Investigación en Síntesis Quı́mica, Universidad de La Rioja, 26006, Logroño, Spain.
Hematology and Hemotherapy Service, Cruces University Hospital, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain.
Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903, Barakaldo, Bizkaia, Spain. [e-mail].
Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain. [e-mail].
Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain. [e-mail].
Genovis AB, Box 790, 22007, Lund, Sweden. [e-mail].
Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903, Barakaldo, Bizkaia, Spain. [e-mail].
Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain. [e-mail].
Ikerbasque, Basque Foundation for Science, 48009, Bilbao, 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

Macromolecule Content 

• Total Structure Weight: 87.84 kDa 
• Atom Count: 6,012 
• Modeled Residue Count: 761 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH95 family alpha-1,2-fucosidase	A	790	Akkermansia muciniphila ATCC BAA-835	Mutation(s): 1  Gene Names: Amuc_1120
UniProt
Find proteins for B2UR61 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc)) Explore B2UR61  Go to UniProtKB:  B2UR61

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.582	α = 90
b = 87.507	β = 102.86
c = 95.586	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Anso, I., Cifuente, J.O., Trastoy, B., Guerin, M.E.

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Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness (MINECO)	Spain	--

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description