5E7H

Crystal structure of domains CD (residues 230-489) of Bacova_02650


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont.

Tauzin, A.S.Kwiatkowski, K.J.Orlovsky, N.I.Smith, C.J.Creagh, A.L.Haynes, C.A.Wawrzak, Z.Brumer, H.Koropatkin, N.M.

(2016) mBio 7: e02134-e02115

  • DOI: https://doi.org/10.1128/mBio.02134-15
  • Primary Citation of Related Structures:  
    5E75, 5E76, 5E7G, 5E7H

  • PubMed Abstract: 

    Polysaccharide utilization loci (PUL) within the genomes of resident human gut Bacteroidetes are central to the metabolism of the otherwise indigestible complex carbohydrates known as "dietary fiber." However, functional characterization of PUL lags significantly behind sequencing efforts, which limits physiological understanding of the human-bacterial symbiosis. In particular, the molecular basis of complex polysaccharide recognition, an essential prerequisite to hydrolysis by cell surface glycosidases and subsequent metabolism, is generally poorly understood. Here, we present the biochemical, structural, and reverse genetic characterization of two unique cell surface glycan-binding proteins (SGBPs) encoded by a xyloglucan utilization locus (XyGUL) from Bacteroides ovatus, which are integral to growth on this key dietary vegetable polysaccharide. Biochemical analysis reveals that these outer membrane-anchored proteins are in fact exquisitely specific for the highly branched xyloglucan (XyG) polysaccharide. The crystal structure of SGBP-A, a SusD homolog, with a bound XyG tetradecasaccharide reveals an extended carbohydrate-binding platform that primarily relies on recognition of the β-glucan backbone. The unique, tetra-modular structure of SGBP-B is comprised of tandem Ig-like folds, with XyG binding mediated at the distal C-terminal domain. Despite displaying similar affinities for XyG, reverse-genetic analysis reveals that SGBP-B is only required for the efficient capture of smaller oligosaccharides, whereas the presence of SGBP-A is more critical than its carbohydrate-binding ability for growth on XyG. Together, these data demonstrate that SGBP-A and SGBP-B play complementary, specialized roles in carbohydrate capture by B. ovatus and elaborate a model of how vegetable xyloglucans are accessed by the Bacteroidetes


  • Organizational Affiliation

    Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IPT/TIG domain-containing protein BACOVA_02650260Bacteroides ovatus ATCC 8483Mutation(s): 0 
Gene Names: BACOVA_02650
UniProt
Find proteins for A7LXT4 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153))
Explore A7LXT4 
Go to UniProtKB:  A7LXT4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7LXT4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT
Query on FMT

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.09α = 90
b = 87.09β = 90
c = 201.56γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references
  • Version 1.2: 2016-08-17
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description