6DMF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 2.0 of the entry. See complete history


Literature

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: 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 ...

    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

    Department of Botany, University of British Columbia, 3200 University Boulevard, Vancouver, BC, V6T 1Z4, Canada. brumer@msl.ubc.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mixed-linkage glucan utilization locus (MLGUL) SGBP-B
A, B, C, D, E, F, G, H, I, J
A, B, C, D, E, F, G, H, I, J
520Bacteroides ovatus ATCC 8483Mutation(s): 0 
Gene Names: BACOVA_02743
UniProt
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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranoseK 5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G91683DU
GlyCosmos:  G91683DU
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
L, M, N, O, P, Q, R, S, T
L, M, N, O, P, Q, R, S, T
6N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G09454VW
GlyCosmos:  G09454VW
GlyGen:  G09454VW
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth B],
CA [auth B],
JB [auth J],
W [auth A],
X [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
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]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
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]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900016
Query on PRD_900016
Kbeta-cellopentaoseOligosaccharide / Metabolism Ligand Interaction
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900020
Query on PRD_900020
L, M, N, O, P, Q, R, S, Tbeta-cellohexaoseOligosaccharide / Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
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