5JVK

Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2.

Ali-Ahmad, A.Garron, M.L.Zamboni, V.Lenfant, N.Nurizzo, D.Henrissat, B.Berrin, J.G.Bourne, Y.Vincent, F.

(2017) J. Struct. Biol. 197: 227-235

  • DOI: 10.1016/j.jsb.2016.11.004

  • PubMed Abstract: 
  • Bacteria from the human gut are equipped with an arsenal of carbohydrate-active enzymes that degrade dietary and host-derived glycans. In this study, we present the 2.5Å resolution crystal structure of a member (GH39wh2) from the human gut bacteria B ...

    Bacteria from the human gut are equipped with an arsenal of carbohydrate-active enzymes that degrade dietary and host-derived glycans. In this study, we present the 2.5Å resolution crystal structure of a member (GH39wh2) from the human gut bacteria Bacteroides cellulosilyticus WH2 representative of a new subgroup within family GH39. Together with 6 other GHs, GH39wh2 belongs to a polysaccharide utilization locus (PUL) that could be involved in detecting, binding and hydrolysing a specific carbohydrate species from the intestinal tract. GH39wh2 shares a similar architecture as other members of family GH39 dominated by a typical (β/α)8-barrel fold harboring the catalytic residues and decorated by β-sandwich accessory domains. The GH39wh2 structure unveils an atypical shallow groove rather than a deep pocket due to drastic rearrangements in surface loops surrounding the catalytic interface. These structural adaptations seem to favour recognition of large branched substrates and may explain the lack of activity of GH39wh2 toward small xylose-based and other typical substrates from GH39 members, emphasizing the molecular diversity within the GH39 family. A phylogenetic analysis of the entire GH39 family assigns GH39wh2 as a new subgroup, consistent with the extensive remodelling of the active site region that may confer new substrate specificity toward a complex glycan chain.


    Organizational Affiliation

    CNRS, Aix Marseille Univ, AFMB, Marseille, France; INRA, USC 1408, AFMB, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, B, C
587Bacteroides cellulosilyticusMutation(s): 0 
Find proteins for A0A0N7IFL6 (Bacteroides cellulosilyticus)
Go to UniProtKB:  A0A0N7IFL6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CXS
Query on CXS

Download SDF File 
Download CCD File 
B, C
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 157.540α = 90.00
b = 157.540β = 90.00
c = 155.644γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
SHARPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Vaincre la mucoviscidoseFrance--

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Database references