7ZNS

Inactive D62N mutant of BT1760 Endo-acting levanase from Bacteroides thetaiotaomicron VPI-5482


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes.

White, J.B.R.Silale, A.Feasey, M.Heunis, T.Zhu, Y.Zheng, H.Gajbhiye, A.Firbank, S.Basle, A.Trost, M.Bolam, D.N.van den Berg, B.Ranson, N.A.

(2023) Nature 618: 583-589

  • DOI: https://doi.org/10.1038/s41586-023-06146-w
  • Primary Citation of Related Structures:  
    7ZNR, 7ZNS, 8A9Y, 8AA0, 8AA1, 8AA2, 8AA3, 8AA4

  • PubMed Abstract: 

    Bacteroidetes are abundant members of the human microbiota, utilizing a myriad of diet- and host-derived glycans in the distal gut 1 . Glycan uptake across the bacterial outer membrane of these bacteria is mediated by SusCD protein complexes, comprising a membrane-embedded barrel and a lipoprotein lid, which is thought to open and close to facilitate substrate binding and transport. However, surface-exposed glycan-binding proteins and glycoside hydrolases also play critical roles in the capture, processing and transport of large glycan chains. The interactions between these components in the outer membrane are poorly understood, despite being crucial for nutrient acquisition by our colonic microbiota. Here we show that for both the levan and dextran utilization systems of Bacteroides thetaiotaomicron, the additional outer membrane components assemble on the core SusCD transporter, forming stable glycan-utilizing machines that we term utilisomes. Single-particle cryogenic electron microscopy structures in the absence and presence of substrate reveal concerted conformational changes that demonstrate the mechanism of substrate capture, and rationalize the role of each component in the utilisome.


  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 32
A, B
523Bacteroides thetaiotaomicron VPI-5482Mutation(s): 1 
Gene Names: BT_1760
UniProt
Find proteins for Q8A6W6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A6W6 
Go to UniProtKB:  Q8A6W6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A6W6
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose
C, D, E
3N/A
Glycosylation Resources
GlyTouCan:  G30220AI
GlyCosmos:  G30220AI
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-6)-beta-D-fructofuranose
F
2N/A
Glycosylation Resources
GlyTouCan:  G51829YA
GlyCosmos:  G51829YA
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
AA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.5α = 90
b = 175.5β = 90
c = 214.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
Cootmodel building
MolProbitymodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/F014163/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release