8PXT | pdb_00008pxt

Targeting extended blood antigens by Akkermansia muciniphila enzymes unveils a missing link for generating universal donor blood

PDB DOI: https://doi.org/10.2210/pdb8PXT/pdb

Classification: HYDROLASE
Organism(s): Akkermansia muciniphila
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-24 Released: 2024-02-28
Deposition Author(s): Jensen, M., Abou Hachem, M., Morth, J.P.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.210 (Depositor), 0.213 (DCC)
R-Value Work:
0.180 (Depositor), 0.182 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Akkermansia muciniphila exoglycosidases target extended blood group antigens to generate ABO-universal blood.

Jensen, M., Stenfelt, L., Ricci Hagman, J., Pichler, M.J., Weikum, J., Nielsen, T.S., Hult, A., Morth, J.P., Olsson, M.L., Abou Hachem, M.

(2024) Nat Microbiol 9: 1176-1188

PubMed: 38684911 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41564-024-01663-4
Primary Citation Related Structures:
8PVS, 8PXT, 8PXU, 8PXV

PubMed Abstract:
Matching donor and recipient blood groups based on red blood cell (RBC) surface ABO glycans and antibodies in plasma is crucial to avoid potentially fatal reactions during transfusions. Enzymatic conversion of RBC glycans to the universal group O is an attractive solution to simplify blood logistics and prevent ABO-mismatched transfusions. The gut symbiont Akkermansia muciniphila can degrade mucin O-glycans including ABO epitopes. Here we biochemically evaluated 23 Akkermansia glycosyl hydrolases and identified exoglycosidase combinations which efficiently transformed both A and B antigens and four of their carbohydrate extensions. Enzymatic removal of canonical and extended ABO antigens on RBCs significantly improved compatibility with group O plasmas, compared to conversion of A or B antigens alone. Finally, structural analyses of two B-converting enzymes identified a previously unknown putative carbohydrate-binding module. This study demonstrates the potential utility of mucin-degrading gut bacteria as valuable sources of enzymes for production of universal blood for transfusions.

Organizational Affiliation

Department of Biotechnology & Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.

Macromolecule Content

Total Structure Weight: 221.43 kDa
Atom Count: 15,667
Modeled Residue Count: 1,905
Deposited Residue Count: 1,965
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A, B, C	655	Akkermansia muciniphila	Mutation(s): 0 Gene Names: Amuc_0369 EC: 3.2.1.52
UniProt
Find proteins for B2UN02 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc)) Explore B2UN02 Go to UniProtKB: B2UN02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2UN02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NGA (Subject of Investigation/LOI) Query on NGA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth C], L [auth C]	2-acetamido-2-deoxy-beta-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-JAJWTYFOSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	G [auth A], H [auth A], M [auth C], N [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C] Focus chain N [auth C]