4X6K

Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with Siastatin B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation.

Tailford, L.E.Owen, C.D.Walshaw, J.Crost, E.H.Hardy-Goddard, J.Le Gall, G.de Vos, W.M.Taylor, G.L.Juge, N.

(2015) Nat Commun 6: 7624-7624

  • DOI: 10.1038/ncomms8624
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut. Alterations in mucosal carbohydrate availability impact on the composition of microbial spec ...

    The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut. Alterations in mucosal carbohydrate availability impact on the composition of microbial species. Ruminococcus gnavus is a commensal anaerobe present in the gastrointestinal tract of >90% of humans and overrepresented in inflammatory bowel diseases (IBD). Using a combination of genomics, enzymology and crystallography, we show that the mucin-degrader R. gnavus ATCC 29149 strain produces an intramolecular trans-sialidase (IT-sialidase) that cleaves off terminal α2-3-linked sialic acid from glycoproteins, releasing 2,7-anhydro-Neu5Ac instead of sialic acid. Evidence of IT-sialidases in human metagenomes indicates that this enzyme occurs in healthy subjects but is more prevalent in IBD metagenomes. Our results uncover a previously unrecognized enzymatic activity in the gut microbiota, which may contribute to the adaptation of intestinal bacteria to the mucosal environment in health and disease.


    Organizational Affiliation

    1] Laboratory of Microbiology, Wageningen UR, Building 316, Dreijenplein 10, 6703 HB Wageningen, The Netherlands [2] Departments of Bacteriology and Immunology and Veterinary Bioscience, University of Helsinki, PO Box 66, FI-00014 Helsinki, Finland.,The Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.,1] The Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK [2] School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK.,Biomolecular Sciences Building, University of St Andrews, St Andrews KY16 9ST, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anhydrosialidase
A
486N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3XR
Query on 3XR

Download SDF File 
Download CCD File 
A
(2S,3R,4S,5S)-2-(acetylamino)-5-carboxy-3,4-dihydroxypiperidinium
C8 H15 N2 O5
DQTKLICLJUKNCG-ZTYPAOSTSA-O
 Ligand Interaction
ACE
Query on ACE

Download SDF File 
Download CCD File 
A
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3XRIC50: 4870 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 99.109α = 90.00
b = 99.109β = 90.00
c = 131.708γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004529/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L008602/1

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 2.0: 2017-08-30
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations