8BMZ | pdb_00008bmz

Bacteroides thetaiotaomicron surface lipoprotein BT1954 bound to adenosylcobalamin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.268 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.223 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8BMZ

Ligand Structure Quality Assessment 


This is version 1.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 83.65 kDa 
  • Atom Count: 5,923 
  • Modeled Residue Count: 664 
  • Deposited Residue Count: 686 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative surface layer protein
A, B
343Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_1954
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B1Z
(Subject of Investigation/LOI)

Query on B1Z



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
Adenosylcobalamin
C72 H101 Co N18 O17 P
NAGDYSDXWHSJMC-OUCXYWSSSA-M
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.268 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.223 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.723α = 90
b = 58.709β = 104.132
c = 101.894γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT 214222/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Refinement description