Sialidase26 apo

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

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This is version 1.4 of the entry. See complete history


Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates.

Zaramela, L.S.Martino, C.Alisson-Silva, F.Rees, S.D.Diaz, S.L.Chuzel, L.Ganatra, M.B.Taron, C.H.Secrest, P.Zuniga, C.Huang, J.Siegel, D.Chang, G.Varki, A.Zengler, K.

(2019) Nat Microbiol 4: 2082-2089

  • DOI: https://doi.org/10.1038/s41564-019-0564-9
  • Primary Citation of Related Structures:  
    6MNJ, 6MRV, 6MRX, 6MYV

  • PubMed Abstract: 

    Dietary habits have been associated with alterations of the human gut resident microorganisms contributing to obesity, diabetes and cancer 1 . In Western diets, red meat is a frequently eaten food 2 , but long-term consumption has been associated with increased risk of disease 3,4 . Red meat is enriched in N-glycolylneuraminic acid (Neu5Gc) that cannot be synthesized by humans 5 . However, consumption can cause Neu5Gc incorporation into cell surface glycans 6 , especially in carcinomas 4,7 . As a consequence, an inflammatory response is triggered when Neu5Gc-containing glycans encounter circulating anti-Neu5Gc antibodies 8,9 . Although bacteria can use free sialic acids as a nutrient source 10-12 , it is currently unknown if gut microorganisms contribute to releasing Neu5Gc from food. We found that a Neu5Gc-rich diet induces changes in the gut microbiota, with Bacteroidales and Clostridiales responding the most. Genome assembling of mouse and human shotgun metagenomic sequencing identified bacterial sialidases with previously unobserved substrate preference for Neu5Gc-containing glycans. X-ray crystallography revealed key amino acids potentially contributing to substrate preference. Additionally, we verified that mouse and human sialidases were able to release Neu5Gc from red meat. The release of Neu5Gc from red meat using bacterial sialidases could reduce the risk of inflammatory diseases associated with red meat consumption, including colorectal cancer 4 and atherosclerosis 13 .

  • Organizational Affiliation

    Department of Pediatrics, University of California, San Diego, CA, USA. kzengler@ucsd.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
553bacteriumMutation(s): 0 
Find proteins for A0A4S2B4D9 (Bacteroides acidifaciens)
Explore A0A4S2B4D9 
Go to UniProtKB:  A0A4S2B4D9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4S2B4D9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.476α = 90
b = 79.817β = 100.918
c = 260.811γ = 90
Software Package:
Software NamePurpose
BOSdata collection
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1444435

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description