6RAB

Ruminococcus gnavus sialic acid aldolase Wild Type


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut.

Bell, A.Brunt, J.Crost, E.Vaux, L.Nepravishta, R.Owen, C.D.Latousakis, D.Xiao, A.Li, W.Chen, X.Walsh, M.A.Claesen, J.Angulo, J.Thomas, G.H.Juge, N.

(2019) Nat Microbiol 4: 2393-2404

  • DOI: https://doi.org/10.1038/s41564-019-0590-7
  • Primary Citation of Related Structures:  
    6RAB, 6RB7, 6RD1

  • PubMed Abstract: 

    Sialic acid (N-acetylneuraminic acid (Neu5Ac)) is commonly found in the terminal location of colonic mucin glycans where it is a much-coveted nutrient for gut bacteria, including Ruminococcus gnavus. R. gnavus is part of the healthy gut microbiota in humans, but it is disproportionately represented in diseases. There is therefore a need to understand the molecular mechanisms that underpin the adaptation of R. gnavus to the gut. Previous in vitro research has demonstrated that the mucin-glycan-foraging strategy of R. gnavus is strain dependent and is associated with the expression of an intramolecular trans-sialidase, which releases 2,7-anhydro-Neu5Ac, rather than Neu5Ac, from mucins. Here, we unravelled the metabolism pathway of 2,7-anhydro-Neu5Ac in R. gnavus that is underpinned by the exquisite specificity of the sialic transporter for 2,7-anhydro-Neu5Ac and by the action of an oxidoreductase that converts 2,7-anhydro-Neu5Ac into Neu5Ac, which then becomes a substrate of a Neu5Ac-specific aldolase. Having generated an R. gnavus nan-cluster deletion mutant that lost the ability to grow on sialylated substrates, we showed that-in gnotobiotic mice colonized with R. gnavus wild-type (WT) and mutant strains-the fitness of the nan mutant was significantly impaired, with a reduced ability to colonize the mucus layer. Overall, we revealed a unique sialic acid pathway in bacteria that has important implications for the spatial adaptation of mucin-foraging gut symbionts in health and disease.


  • Organizational Affiliation

    Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative N-acetylneuraminate lyase
A, B
336Mediterraneibacter gnavus ATCC 29149Mutation(s): 0 
Gene Names: RUMGNA_02692
UniProt
Find proteins for A7B555 (Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9))
Explore A7B555 
Go to UniProtKB:  A7B555
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7B555
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.766α = 90
b = 120.592β = 148.38
c = 88.264γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
AutoPROCdata collection

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M011216/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Database references