6HUS

2'-fucosyllactose and 3-fucosyllactose binding protein from Bifidobacterium longum infantis, bound with 3-fucosyllactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.142 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis.

Sakanaka, M.Hansen, M.E.Gotoh, A.Katoh, T.Yoshida, K.Odamaki, T.Yachi, H.Sugiyama, Y.Kurihara, S.Hirose, J.Urashima, T.Xiao, J.Z.Kitaoka, M.Fukiya, S.Yokota, A.Lo Leggio, L.Abou Hachem, M.Katayama, T.

(2019) Sci Adv 5: eaaw7696-eaaw7696

  • DOI: https://doi.org/10.1126/sciadv.aaw7696
  • Primary Citation of Related Structures:  
    6HUR, 6HUS

  • PubMed Abstract: 

    The human gut microbiota established during infancy has persistent effects on health. In vitro studies have suggested that human milk oligosaccharides (HMOs) in breast milk promote the formation of a bifidobacteria-rich microbiota in infant guts; however, the underlying molecular mechanism remains elusive. Here, we characterized two functionally distinct but overlapping fucosyllactose transporters (FL transporter-1 and -2) from Bifidobacterium longum subspecies infantis . Fecal DNA and HMO consumption analyses, combined with deposited metagenome data mining, revealed that FL transporter-2 is primarily associated with the bifidobacteria-rich microbiota formation in breast-fed infant guts. Structural analyses of the solute-binding protein (SBP) of FL transporter-2 complexed with 2'-fucosyllactose and 3-fucosyllactose, together with phylogenetic analysis of SBP homologs of both FL transporters, highlight a unique adaptation strategy of Bifidobacterium to HMOs, in which the gain-of-function mutations enable FL transporter-2 to efficiently capture major fucosylated HMOs. Our results provide a molecular insight into HMO-mediated symbiosis and coevolution between bifidobacteria and humans.


  • Organizational Affiliation

    Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter substrate-binding protein428Bifidobacterium longum subsp. infantisMutation(s): 0 
Gene Names: BFS25_04965
UniProt
Find proteins for A0A1S2VYK0 (Bifidobacterium longum subsp. infantis)
Explore A0A1S2VYK0 
Go to UniProtKB:  A0A1S2VYK0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S2VYK0
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose-(1-3)-alpha-D-glucopyranose
B
4N/AN/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.142 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.2α = 90
b = 134.2β = 90
c = 59.99γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmarkDFF-4002-00297

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-05-15
    Changes: Data collection, Database references, Derived calculations, Structure summary