› 6n1b

X-ray diffraction
1.3Å resolution

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

Released:
DOI: 10.2210/pdb6n1b/pdb
PDB entry 6n1b coloured by chain, front view.
PDB entry 6n1b coloured by chain, side view.
PDB entry 6n1b coloured by chain, top view.
Source organism: Flavonifractor plautii
Primary publication:
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 SJ, Kizhakkedathu JN, Withers SG
Nat Microbiol 4 1475-1485 (2019)
PMID: 31182795

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124694 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
F5/8 type C domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 503 amino acids
Theoretical weight: 55.8 KDa
Source organism: Flavonifractor plautii
Expression system: Escherichia coli
UniProt:
  • Canonical: G9YSP4 (Residues: 28-509; Coverage: 65%)
Gene name: HMPREF0372_02552
Sequence domains: Bacterial Ig-like domain (group 2)

Ligands and Environments

Carbohydrate polymer : NEW Components: GAL, FUC, GLA
Carbohydrate polymer
2 bound ligands:
Ligand CA 4 x CA
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P212121
Unit cell:
a: 51.71Å b: 69.24Å c: 104.81Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.147 0.146 0.162
Expression system: Escherichia coli

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Citations

9 review citations

Carbohydrate-active enzymes (CAZymes) in the gut microbiome.
Wardman et al. (2022)
8 more