4C91

Evidence that GH115 alpha-glucuronidase activity is dependent on conformational flexibility


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Evidence that Gh115 Alpha-Glucuronidase Activity is Dependent on Conformational Flexibility

Rogowski, A.Basle, A.Farinas, C.S.Solovyova, A.Mortimer, J.C.Dupree, P.Gilbert, H.J.Bolam, D.N.

(2014) J.Biol.Chem. 289: 53

  • DOI: 10.1074/jbc.M113.525295
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The microbial degradation of the plant cell wall is an important biological process that is highly relevant to environmentally significant industries such as the bioenergy and biorefining sectors. A major component of the wall is glucuronoxylan, a β1 ...

    The microbial degradation of the plant cell wall is an important biological process that is highly relevant to environmentally significant industries such as the bioenergy and biorefining sectors. A major component of the wall is glucuronoxylan, a β1,4-linked xylose polysaccharide that is decorated with α-linked glucuronic and/or methylglucuronic acid (GlcA/MeGlcA). Recently three members of a glycoside hydrolase family, GH115, were shown to hydrolyze MeGlcA side chains from the internal regions of xylan, an activity that has not previously been described. Here we show that a dominant member of the human microbiota, Bacteroides ovatus, contains a GH115 enzyme, BoAgu115A, which displays glucuronoxylan α-(4-O-methyl)-glucuronidase activity. The enzyme is significantly more active against substrates in which the xylose decorated with GlcA/MeGlcA is flanked by one or more xylose residues. The crystal structure of BoAgu115A revealed a four-domain protein in which the active site, comprising a pocket that abuts a cleft-like structure, is housed in the second domain that adopts a TIM barrel-fold. The third domain, a five-helical bundle, and the C-terminal β-sandwich domain make inter-chain contacts leading to protein dimerization. Informed by the structure of the enzyme in complex with GlcA in its open ring form, in conjunction with mutagenesis studies, the potential substrate binding and catalytically significant amino acids were identified. Based on the catalytic importance of residues located on a highly flexible loop, the enzyme is required to undergo a substantial conformational change to form a productive Michaelis complex with glucuronoxylan.


    Organizational Affiliation

    From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH United Kingdom and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-GLUCURONIDASE GH115
A, B
856Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153)Mutation(s): 0 
Find proteins for A7M022 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153))
Go to UniProtKB:  A7M022
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
REL
Query on REL

Download SDF File 
Download CCD File 
A
D-glucuronic acid
D-Glucuronate, alpha-D-glucofuranuronic acid
C6 H10 O7
IAJILQKETJEXLJ-QTBDOELSSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.040α = 90.00
b = 130.290β = 90.00
c = 190.170γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
iMOSFLMdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references
  • Version 1.2: 2014-01-15
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Data collection