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

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways.

Pichler, M.J.Yamada, C.Shuoker, B.Alvarez-Silva, C.Gotoh, A.Leth, M.L.Schoof, E.Katoh, T.Sakanaka, M.Katayama, T.Jin, C.Karlsson, N.G.Arumugam, M.Fushinobu, S.Abou Hachem, M.

(2020) Nat Commun 11: 3285-3285

  • DOI: https://doi.org/10.1038/s41467-020-17075-x
  • Primary Citation of Related Structures:  
    6KQS, 6KQT

  • PubMed Abstract: 

    The early life human gut microbiota exerts life-long health effects on the host, but the mechanisms underpinning its assembly remain elusive. Particularly, the early colonization of Clostridiales from the Roseburia-Eubacterium group, associated with protection from colorectal cancer, immune- and metabolic disorders is enigmatic. Here, we describe catabolic pathways that support the growth of Roseburia and Eubacterium members on distinct human milk oligosaccharides (HMOs). The HMO pathways, which include enzymes with a previously unknown structural fold and specificity, were upregulated together with additional glycan-utilization loci during growth on selected HMOs and in co-cultures with Akkermansia muciniphila on mucin, suggesting an additional role in enabling cross-feeding and access to mucin O-glycans. Analyses of 4599 Roseburia genomes underscored the preponderance and diversity of the HMO utilization loci within the genus. The catabolism of HMOs by butyrate-producing Clostridiales may contribute to the competitiveness of this group during the weaning-triggered maturation of the microbiota.

  • Organizational Affiliation

    Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Lyngby, Denmark.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
lacto-N-biosidase665Eubacterium ramulus ATCC 29099Mutation(s): 0 
Gene Names: HMPREF0373_02965
Find proteins for U2PDT9 (Eubacterium ramulus ATCC 29099)
Explore U2PDT9 
Go to UniProtKB:  U2PDT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU2PDT9
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G00056MO
GlyCosmos:  G00056MO
GlyGen:  G00056MO
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.295α = 90
b = 132.295β = 90
c = 82.2γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-27
    Changes: Data collection, Database references, Structure summary