Crystal structure of an N-acetylgalactosamine deacetylase from F. plautii in complex with blood group B trisaccharide

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

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An enzymatic pathway in the human gut microbiome that converts A to universal O type blood.

Rahfeld, P.Sim, L.Moon, H.Constantinescu, I.Morgan-Lang, C.Hallam, S.J.Kizhakkedathu, J.N.Withers, S.G.

(2019) Nat Microbiol 4: 1475-1485

  • DOI: https://doi.org/10.1038/s41564-019-0469-7
  • Primary Citation of Related Structures:  
    6N1A, 6N1B

  • PubMed Abstract: 

    Access to efficient enzymes that can convert A and B type red blood cells to 'universal' donor O would greatly increase the supply of blood for transfusions. Here we report the functional metagenomic screening of the human gut microbiome for enzymes that can remove the cognate A and B type sugar antigens. Among the genes encoded in our library of 19,500 expressed fosmids bearing gut bacterial DNA, we identify an enzyme pair from the obligate anaerobe Flavonifractor plautii that work in concert to efficiently convert the A antigen to the H antigen of O type blood, via a galactosamine intermediate. The X-ray structure of the N-acetylgalactosamine deacetylase reveals the active site and mechanism of the founding member of an esterase family. The galactosaminidase expands activities within the CAZy family GH36. Their ability to completely convert A to O of the same rhesus type at very low enzyme concentrations in whole blood will simplify their incorporation into blood transfusion practice, broadening blood supply.

  • Organizational Affiliation

    Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada. withers@chem.ubc.ca.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbohydrate-binding protein503Flavonifractor plautiiMutation(s): 0 
Gene Names: A4U99_12080
Find proteins for G9YSP4 (Flavonifractor plautii ATCC 29863)
Explore G9YSP4 
Go to UniProtKB:  G9YSP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9YSP4
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G47548GA
GlyCosmos:  G47548GA
GlyGen:  G47548GA
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.71α = 90
b = 69.24β = 90
c = 104.81γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-136940

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary