› 6tr4

X-ray diffraction
1.45Å resolution

Ruminococcus gnavus GH29 fucosidase E1_10125 D221A mutant in complex with fucose

Released:
DOI: 10.2210/pdb6tr4/pdb
PDB entry 6tr4 coloured by chain, front view.
PDB entry 6tr4 coloured by chain, side view.
PDB entry 6tr4 coloured by chain, top view.
Source organism: [Ruminococcus] gnavus E1
Primary publication:
Fucosidases from the human gut symbiont Ruminococcus gnavus.
Wu H, Rebello O, Crost EH, Owen CD, Walpole S, Bennati-Granier C, Ndeh D, Monaco S, Hicks T, Colvile A, Urbanowicz PA, Walsh MA, Angulo J, Spencer DIR, Juge N
Cell Mol Life Sci 78 675-693 (2021)
PMID: 32333083

Function and Biology Details

Reaction catalysed: 
4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + H(2)O = 4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-105796 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
F5/8 type C domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 552 amino acids
Theoretical weight: 61.66 KDa
Source organism: [Ruminococcus] gnavus E1
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A6N3BKT0 (Residues: 32-583; Coverage: 29%)
Gene names: RGLFYP19_01198, hypBA2
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand FUL 1 x FUL
Ligand FUC 2 x FUC
Ligand MG 5 x MG
Ligand CA 6 x CA
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P1
Unit cell:
a: 49.78Å b: 74.06Å c: 76.509Å
α: 82.47° β: 80.43° γ: 70.41°
R-values:
R R work R free
0.142 0.141 0.16
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Gold standard for nutrition: a review of human milk oligosaccharide and its effects on infant gut microbiota.
Zhang et al. (2021)
5 more

3 mentions without citation

Ruminococcus gnavus: friend or foe for human health.
Crost et al. (2023)
2 more