4UFC

Crystal structure of the GH95 enzyme BACOVA_03438

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Glycan Complexity Dictates Microbial Resource Allocation in the Large Intestine.

Rogowski, A., Briggs, J.A., Mortimer, J.C., Tryfona, T., Terrapon, N., Lowe, E.C., Basle, A., Morland, C., Day, A.M., Zheng, H., Rogers, T.E., Thompson, P., Hawkins, A.R., Yadav, M.P., Henrissat, B., Martens, E.C., Dupree, P., Gilbert, H.J., Bolam, D.N.

(2015) Nat.Commun. 6: 7481

  • DOI: 10.1038/ncomms8481

  • PubMed Abstract: 

    • The structure of the human gut microbiota is controlled primarily through the degradation of complex dietary carbohydrates, but the extent to which carbohydrate breakdown products are shared between members of the microbiota is unclear. We show here, ...

    The structure of the human gut microbiota is controlled primarily through the degradation of complex dietary carbohydrates, but the extent to which carbohydrate breakdown products are shared between members of the microbiota is unclear. We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members of the microbiota, such as Bacteroides ovatus, is dependent on the complexity of the target glycan. Characterization of the extensive xylan degrading apparatus expressed by B. ovatus reveals that the breakdown of the polysaccharide by the human gut microbiota is significantly more complex than previous models suggested, which were based on the deconstruction of xylans containing limited monosaccharide side chains. Our report presents a highly complex and dynamic xylan degrading apparatus that is fine-tuned to recognize the different forms of the polysaccharide presented to the human gut microbiota.

    Organizational Affiliation: 

    Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GH95
A, B
811Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153)Mutation(s): 0 
Find proteins for A7M011 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153))
Go to UniProtKB:  A7M011
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
GIV
Query on GIV
Download SDF File 
Download CCD File 
A, B
BETA-L-GALACTOPYRANOSE
C6 H12 O6
WQZGKKKJIJFFOK-KGJVWPDLSA-N
 Ligand Interaction
CAC
Query on CAC
Download SDF File 
Download CCD File 
A, B
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.692α = 90.00
b = 179.117β = 90.00
c = 205.181γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release