Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-A with cellohexaose

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus.

Tamura, K.Foley, M.H.Gardill, B.R.Dejean, G.Schnizlein, M.Bahr, C.M.E.Louise Creagh, A.van Petegem, F.Koropatkin, N.M.Brumer, H.

(2019) Cell Mol Life Sci 76: 4319-4340

  • DOI: https://doi.org/10.1007/s00018-019-03115-3
  • Primary Citation of Related Structures:  
    6DMF, 6E57, 6E60, 6E61, 6E9B

  • PubMed Abstract: 

    The human gut microbiota, which underpins nutrition and systemic health, is compositionally sensitive to the availability of complex carbohydrates in the diet. The Bacteroidetes comprise a dominant phylum in the human gut microbiota whose members thrive on dietary and endogenous glycans by employing a diversity of highly specific, multi-gene polysaccharide utilization loci (PUL), which encode a variety of carbohydrases, transporters, and sensor/regulators. PULs invariably also encode surface glycan-binding proteins (SGBPs) that play a central role in saccharide capture at the outer membrane. Here, we present combined biophysical, structural, and in vivo characterization of the two SGBPs encoded by the Bacteroides ovatus mixed-linkage β-glucan utilization locus (MLGUL), thereby elucidating their key roles in the metabolism of this ubiquitous dietary cereal polysaccharide. In particular, molecular insight gained through several crystallographic complexes of SGBP-A and SGBP-B with oligosaccharides reveals that unique shape complementarity of binding platforms underpins specificity for the kinked MLG backbone vis-à-vis linear β-glucans. Reverse-genetic analysis revealed that both the presence and binding ability of the SusD homolog BoSGBP MLG -A are essential for growth on MLG, whereas the divergent, multi-domain BoSGBP MLG -B is dispensable but may assist in oligosaccharide scavenging from the environment. The synthesis of these data illuminates the critical role SGBPs play in concert with other MLGUL components, reveals new structure-function relationships among SGBPs, and provides fundamental knowledge to inform future (meta)genomic, biochemical, and microbiological analyses of the human gut microbiota.

  • Organizational Affiliation

    Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada. brumer@msl.ubc.ca.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mixed-linkage glucan utilization locus (MLGUL) SGBP-B
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
520Bacteroides 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
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G91683DU
GlyCosmos:  G91683DU
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
L, M, N, O, P
L, M, N, O, P, Q, R, S, T
Glycosylation Resources
GlyTouCan:  G09454VW
GlyCosmos:  G09454VW
GlyGen:  G09454VW
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth B],
CA [auth B],
JB [auth J],
W [auth A],
X [auth A]
C4 H10 O3
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth G]
DA [auth B]
DB [auth H]
EA [auth B]
GB [auth I]
AB [auth G],
DA [auth B],
DB [auth H],
EA [auth B],
GB [auth I],
HA [auth C],
IA [auth C],
JA [auth C],
MA [auth D],
PA [auth E],
QA [auth E],
RA [auth E],
SA [auth E],
WA [auth G],
XA [auth G],
Y [auth A],
YA [auth G],
ZA [auth G]
C2 H6 O2
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth B]
CB [auth H]
FB [auth I]
GA [auth C]
IB [auth J]
AA [auth B],
CB [auth H],
FB [auth I],
GA [auth C],
IB [auth J],
LA [auth D],
OA [auth E],
UA [auth F],
V [auth A]
C2 H3 O2
Query on MG

Download Ideal Coordinates CCD File 
BB [auth H]
EB [auth I]
FA [auth C]
HB [auth J]
KA [auth D]
BB [auth H],
EB [auth I],
FA [auth C],
HB [auth J],
KA [auth D],
NA [auth E],
TA [auth F],
U [auth A],
VA [auth G],
Z [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.845α = 90
b = 228.845β = 90
c = 246.517γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118475

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary