6N1B | pdb_00006n1b

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

• PDB DOI: https://doi.org/10.2210/pdb6N1B/pdb

• Classification: HYDROLASE
• Organism(s): Flavonifractor plautii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-08 Released: 2019-06-12 
• Deposition Author(s): Sim, L., Rahfeld, P., Withers, S.G.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.162 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 31182795 
• DOI: https://doi.org/10.1038/s41564-019-0469-7
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
Department of Pathology and Laboratory Medicine, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
Graduate Program in Bioinformatics, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada. [e-mail].
Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada. [e-mail].
Department of Biochemistry, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 56.73 kDa 
• Atom Count: 3,485 
• Modeled Residue Count: 385 
• Deposited Residue Count: 503 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbohydrate-binding protein	A	503	Flavonifractor plautii	Mutation(s): 0  Gene Names: A4U99_12080
UniProt
Find proteins for G9YSP4 (Flavonifractor plautii ATCC 29863) Explore G9YSP4  Go to UniProtKB:  G9YSP4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G47548GA GlyCosmos: G47548GA GlyGen: G47548GA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.162 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.71	α = 90
b = 69.24	β = 90
c = 104.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Sim, L., Rahfeld, P., Withers, S.G.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-136940

Revision History  

• 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