8BMX

Bacteroides thetaiotaomicron B12 TonB dependent transporter in complex with a surface lipoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.72 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B 12 uptake in gut Bacteroides.

Abellon-Ruiz, J.Jana, K.Silale, A.Frey, A.M.Basle, A.Trost, M.Kleinekathofer, U.van den Berg, B.

(2023) Nat Commun 14: 4714-4714

  • DOI: https://doi.org/10.1038/s41467-023-40427-2
  • Primary Citation of Related Structures:  
    8BLW, 8BMX, 8BMY, 8BMZ, 8BN0, 8OKV, 8P97, 8P98

  • PubMed Abstract: 

    Vitamin B 12 (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition for this keystone micronutrient is severe. Contrasting with Enterobacteria, members of the dominant genus Bacteroides often encode several BtuB vitamin B 12 outer membrane transporters together with a conserved array of surface-exposed B 12 -binding lipoproteins. Here we show that the BtuB transporters from Bacteroides thetaiotaomicron form stable, pedal bin-like complexes with surface-exposed BtuG lipoprotein lids, which bind B 12 with high affinities. Closing of the BtuG lid following B 12 capture causes destabilisation of the bound B 12 by a conserved BtuB extracellular loop, causing translocation of the vitamin to BtuB and subsequent transport. We propose that TonB-dependent, lipoprotein-assisted small molecule uptake is a general feature of Bacteroides spp. that is important for the success of this genus in colonising the human gut.


  • Organizational Affiliation

    Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative TonB-linked outer membrane receptorA [auth C],
B [auth A],
C [auth B]
698Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_1953
Membrane Entity: Yes 
UniProt
Find proteins for Q8A6D1 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A6D1 
Go to UniProtKB:  Q8A6D1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A6D1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
YncE family protein
D, E, F
366Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
UniProt
Find proteins for Q8A6D0 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A6D0 
Go to UniProtKB:  Q8A6D0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A6D0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.72 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 280.25α = 90
b = 154.3β = 106.96
c = 107.51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom214222/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release