Structure of SGBP BO2743 from Bacteroides ovatus in complex with mixed-linked gluco-nonasaccharide

Experimental Data Snapshot

  • Resolution: 1.43 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.162 

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This is version 1.3 of the entry. See complete history


Mapping Molecular Recognition of beta 1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus.

Correia, V.G.Trovao, F.Pinheiro, B.A.Bras, J.L.A.Silva, L.M.Nunes, C.Coimbra, M.A.Liu, Y.Feizi, T.Fontes, C.M.G.A.Mulloy, B.Chai, W.Carvalho, A.L.Palma, A.S.

(2021) Microbiol Spectr 9: e0182621-e0182621

  • DOI: https://doi.org/10.1128/Spectrum.01826-21
  • Primary Citation of Related Structures:  
    7NOX, 7O8C

  • PubMed Abstract: 
  • A multigene polysaccharide utilization locus (PUL) encoding enzymes and surface carbohydrate (glycan)-binding proteins (SGBPs) was recently identified in prominent members of Bacteroidetes in the human gut and characterized in Bacteroides ovatus ...

    A multigene polysaccharide utilization locus (PUL) encoding enzymes and surface carbohydrate (glycan)-binding proteins (SGBPs) was recently identified in prominent members of Bacteroidetes in the human gut and characterized in Bacteroides ovatus. This PUL-encoded system specifically targets mixed-linkage β1,3-1,4-glucans, a group of diet-derived carbohydrates that promote a healthy microbiota and have potential as prebiotics. The BoSGBP MLG -A protein encoded by the BACOVA_2743 gene is a SusD-like protein that plays a key role in the PUL's specificity and functionality. Here, we perform a detailed analysis of the molecular determinants underlying carbohydrate binding by BoSGBP MLG -A, combining carbohydrate microarray technology with quantitative affinity studies and a high-resolution X-ray crystallography structure of the complex of BoSGBP MLG -A with a β1,3-1,4-nonasaccharide. We demonstrate its unique binding specificity toward β1,3-1,4-gluco-oligosaccharides, with increasing binding affinities up to the octasaccharide and dependency on the number and position of β1,3 linkages. The interaction is defined by a 41-Å-long extended binding site that accommodates the oligosaccharide in a mode distinct from that of previously described bacterial β1,3-1,4-glucan-binding proteins. In addition to the shape complementarity mediated by CH-π interactions, a complex hydrogen bonding network complemented by a high number of key ordered water molecules establishes additional specific interactions with the oligosaccharide. These support the twisted conformation of the β-glucan backbone imposed by the β1,3 linkages and explain the dependency on the oligosaccharide chain length. We propose that the specificity of the PUL conferred by BoSGBP MLG -A to import long β1,3-1,4-glucan oligosaccharides to the bacterial periplasm allows Bacteroidetes to outcompete bacteria that lack this PUL for utilization of β1,3-1,4-glucans. IMPORTANCE With the knowledge of bacterial gene systems encoding proteins that target dietary carbohydrates as a source of nutrients and their importance for human health, major efforts are being made to understand carbohydrate recognition by various commensal bacteria. Here, we describe an integrative strategy that combines carbohydrate microarray technology with structural studies to further elucidate the molecular determinants of carbohydrate recognition by BoSGBP MLG -A, a key protein expressed at the surface of Bacteroides ovatus for utilization of mixed-linkage β1,3-1,4-glucans. We have mapped at high resolution interactions that occur at the binding site of BoSGBP MLG -A and provide evidence for the role of key water-mediated interactions for fine specificity and affinity. Understanding at the molecular level how commensal bacteria, such as prominent members of Bacteroidetes , can differentially utilize dietary carbohydrates with potential prebiotic activities will shed light on possible ways to modulate the microbiome to promote human health.

    Organizational Affiliation

    Associate Laboratory i4HB-Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Surface glycan-binding protein BO2743
A, B
598Bacteroides ovatus ATCC 8483Mutation(s): 0 
Gene Names: BACOVA_02743
Find proteins for A7LY27 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153))
Explore A7LY27 
Go to UniProtKB:  A7LY27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7LY27
Protein Feature View
  • Reference Sequence


Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
C, D
9N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G43976CC
GlyCosmos:  G43976CC
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on TAM

Download Ideal Coordinates CCD File 
C7 H17 N O3
 Ligand Interaction
Query on PGE

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AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
H [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
C6 H14 O4
 Ligand Interaction
Query on GOL

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F [auth A],
G [auth A],
X [auth B],
Y [auth B],
Z [auth B]
C3 H8 O3
 Ligand Interaction
Query on AZI

Download Ideal Coordinates CCD File 
FA [auth B]
GA [auth B]
HA [auth B]
IA [auth B]
JA [auth B]
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
 Ligand Interaction
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
V [auth B]
 Ligand Interaction
Query on NA

Download Ideal Coordinates CCD File 
EA [auth B],
L [auth A],
M [auth A]
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 1.43 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.842α = 90
b = 88.437β = 90
c = 156.148γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
STARANISOdata reduction
STARANISOdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Foundation for Science and Technology (FCT)PortugalPTDC/BIA-MIB/31730/2017
Foundation for Science and Technology (FCT)PortugalRECI/BBB-BEP/0124/2012

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Data collection, Database references
  • Version 1.2: 2022-01-05
    Changes: Database references
  • Version 1.3: 2022-01-19
    Changes: Database references