7BIZ

Structure of a B12 binding lipoprotein from Bacteroides thetaiotaomicron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B 12 -Binding Proteins.

Putnam, E.E.Abellon-Ruiz, J.Killinger, B.J.Rosnow, J.J.Wexler, A.G.Folta-Stogniew, E.Wright, A.T.van den Berg, B.Goodman, A.L.

(2022) mBio 13: e0284521-e0284521

  • DOI: https://doi.org/10.1128/mbio.02845-21
  • Primary Citation of Related Structures:  
    7BIZ

  • PubMed Abstract: 

    Human gut commensal Bacteroidetes rely on multiple transport systems to acquire vitamin B 12 and related cobamides for fitness in the gut. In addition to a set of conserved transport proteins, these systems also include a diverse repertoire of additional proteins with unknown function. Here, we report the function and structural characterization of one of these proteins, BtuH, which binds vitamin B 12 directly via a C-terminal globular domain that has no known structural homologs. This protein is required for efficient B 12 transport and competitive fitness in the gut, demonstrating that members of the heterogeneous suite of accessory proteins encoded in Bacteroides cobamide transport system loci can play key roles in vitamin acquisition. IMPORTANCE The gut microbiome is a complex microbial community with important impacts on human health. One of the major groups within the gut microbiome, the Bacteroidetes , rely on their ability to capture vitamin B 12 and related molecules for fitness in the gut. Unlike well-studied model organisms, gut Bacteroidetes genomes often include multiple vitamin B 12 transport systems with a heterogeneous set of components. The role, if any, of these components was unknown. Here, we identify new proteins that play key roles in vitamin B 12 capture in these organisms. Notably, these proteins are associated with some B 12 transport systems and not others (even in the same bacterial strain), suggesting that these systems may assemble into functionally distinct machines to capture vitamin B 12 and related molecules.


  • Organizational Affiliation

    Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale Universitygrid.47100.32 School of Medicine, New Haven, Connecticut, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell surface protein
A, B
501Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q8A6C8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A6C8 
Go to UniProtKB:  Q8A6C8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A6C8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
M [auth B]
POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
CNC (Subject of Investigation/LOI)
Query on CNC

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
CYANOCOBALAMIN
C63 H89 Co N14 O14 P
SYZBZQWSWIJYAR-UVKKECPRSA-M
MES
Query on MES

Download Ideal Coordinates CCD File 
L [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.052α = 90
b = 128.052β = 90
c = 135.051γ = 120
Software Package:
Software NamePurpose
DIALSdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2022-05-04
    Changes: Database references
  • Version 1.3: 2022-05-11
    Changes: Database references
  • Version 1.4: 2024-05-01
    Changes: Data collection, Refinement description