4X4A

Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with 2,7-Anhydro-Neu5Ac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 2.1 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

    The Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anhydrosialidase
A
489N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SKD
Query on SKD

Download SDF File 
Download CCD File 
A
2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID
2,7-ANHYDRO-NEU5AC
C11 H17 N O8
NCMJSVDTRDLWJE-YRMXFSIDSA-N
 Ligand Interaction
ACE
Query on ACE

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Download CCD File 
A
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SKDKi: 2370000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.143 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 99.257α = 90.00
b = 99.257β = 90.00
c = 130.599γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
REFMACrefinement
SCALEPACKdata scaling

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
  • Version 2.1: 2018-11-21
    Type: Data collection, Source and taxonomy