› 6er3

X-ray diffraction
1.37Å resolution

Ruminococcus gnavus IT-sialidase CBM40 bound to alpha2,3 sialyllactose

Released:
DOI: 10.2210/pdb6er3/pdb
PDB entry 6er3 coloured by chain, front view.
PDB entry 6er3 coloured by chain, side view.
PDB entry 6er3 coloured by chain, top view.
Source organism: [Ruminococcus] gnavus ATCC 29149
Primary publication:
Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus.
Owen CD, Tailford LE, Monaco S, Šuligoj T, Vaux L, Lallement R, Khedri Z, Yu H, Lecointe K, Walshaw J, Tribolo S, Horrex M, Bell A, Chen X, Taylor GL, Varki A, Angulo J, Juge N
Nat Commun 8 2196 (2017)
PMID: 29259165

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108236 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
BNR/Asp-box repeat protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 190 amino acids
Theoretical weight: 20.49 KDa
Source organism: [Ruminococcus] gnavus ATCC 29149
Expression system: Escherichia coli
UniProt:
  • Canonical: A7B557 (Residues: 50-237; Coverage: 27%)
Gene name: RUMGNA_02694
Sequence domains: Sialidase, N-terminal domain
Structure domains: Jelly Rolls

Ligands and Environments

Carbohydrate polymer : NEW Components: GAL, SIA
Carbohydrate polymer
1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 48.8Å b: 72.35Å c: 51.52Å
α: 90° β: 105.1° γ: 90°
R-values:
R R work R free
0.151 0.149 0.187
Expression system: Escherichia coli

Quick links

Citations

15 review citations

Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier.
Martens et al. (2018)
14 more

2 mentions without citation

Biochemical and structural basis of sialic acid utilization by gut microbes.
Bell et al. (2023)
1 more