› 6kqt

X-ray diffraction
2Å resolution

Crystal Structure of GH136 lacto-N-biosidase from Eubacterium ramulus - native protein

Released:
DOI: 10.2210/pdb6kqt/pdb
PDB entry 6kqt coloured by chain, front view.
PDB entry 6kqt coloured by chain, side view.
PDB entry 6kqt coloured by chain, top view.
Source organism: Eubacterium ramulus ATCC 29099
Primary publication:
Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways.
Pichler MJ, Yamada C, Shuoker B, Alvarez-Silva C, Gotoh A, Leth ML, Schoof E, Katoh T, Sakanaka M, Katayama T, Jin C, Karlsson NG, Arumugam M, Fushinobu S, Abou Hachem M
Nat Commun 11 3285 (2020)
PMID: 32620774

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-197519 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Right handed beta helix domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 665 amino acids
Theoretical weight: 76.15 KDa
Source organism: Eubacterium ramulus ATCC 29099
Expression system: Escherichia coli
UniProt:
  • Canonical: U2PDT9 (Residues: 1-663; Coverage: 100%)
Gene name: HMPREF0373_02965

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, GAL
Carbohydrate polymer
2 bound ligands:
Ligand PGE 1 x PGE
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P3121
Unit cell:
a: 132.295Å b: 132.295Å c: 82.2Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.145 0.143 0.181
Expression system: Escherichia coli

Quick links

Citations

20 review citations

The Microbiota of the Human Mammary Ecosystem.
Fernández et al. (2020)
19 more

1 mention without citation

O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases.
Labourel et al. (2023)