6HUR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.151 

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Ligand Structure Quality Assessment 


This is version 2.0 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: 10.1126/sciadv.aaw7696
  • Primary Citation of Related Structures:  
    6HUS, 6HUR

  • 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 ...

    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

    Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ABC transporter substrate-binding proteinA428Bifidobacterium longum subsp. infantisMutation(s): 0 
Gene Names: BFS25_04965
UniProt
Find proteins for A0A1S2VYK0 (Bifidobacterium longum subsp. infantis)
Explore A0A1S2VYK0 
Go to UniProtKB:  A0A1S2VYK0
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranoseB3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G94133JU
GlyCosmos:  G94133JU
GlyGen:  G94133JU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.151 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134α = 90
b = 134β = 90
c = 59.7γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHENIXmodel building
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



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