4X47 | pdb_00004x47

Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with Neu5Ac2en


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.273 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4X47

Ligand Structure Quality Assessment 


This is version 2.3 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: https://doi.org/10.1038/ncomms8624
  • Primary Citation Related Structures: 
    4X47, 4X49, 4X4A, 4X6K

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 54.38 kDa 
  • Atom Count: 4,080 
  • Modeled Residue Count: 489 
  • Deposited Residue Count: 489 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Anhydrosialidase489Mediterraneibacter gnavus ATCC 29149Mutation(s): 0 
Gene Names: HMPREF1201_01421
EC: 3.2.1.18

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DAN

Query on DAN



Download:Ideal Coordinates CCD File
B [auth A]2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.273 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.305α = 90
b = 101.305β = 90
c = 131.939γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 2.0: 2017-08-30
    Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
  • Version 2.1: 2018-11-21
    Changes: Data collection, Source and taxonomy
  • Version 2.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations
  • Version 2.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary