6NCX

Crystal structure of GH2 beta-galacturonidase from Eisenbergiella tayi bound to galacturonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selecting a Single Stereocenter: The Molecular Nuances That Differentiate beta-Hexuronidases in the Human Gut Microbiome.

Pellock, S.J.Walton, W.G.Redinbo, M.R.

(2019) Biochemistry 58: 1311-1317

  • DOI: 10.1021/acs.biochem.8b01285
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human gut microbiome is a ripe space for the discovery of new proteins and novel functions. Many genes in the gut microbiome encode glycoside hydrolases that help bacteria scavenge sugars present in the human gut. Glycoside hydrolase family 2 (GH ...

    The human gut microbiome is a ripe space for the discovery of new proteins and novel functions. Many genes in the gut microbiome encode glycoside hydrolases that help bacteria scavenge sugars present in the human gut. Glycoside hydrolase family 2 (GH2) is one group of sugar-scavenging proteins, which includes β-glucuronidases (GUS) and β-galacturonidases (GalAses), enzymes that cleave the sugar conjugates of the epimers glucuronate and galacturonate. Here we structurally and functionally characterize a GH2 GalAse and a hybrid GUS/GalAse, which reveal the molecular details that enable these GHs to differentiate a single stereocenter. First, we characterized a previously annotated GUS from Eisenbergiella tayi and demonstrated that it is, in fact, a GalAse. We determined the crystal structure of this GalAse, identified the key residue that confers GalAse activity, and convert this GalAse into a GUS by mutating a single residue. We performed bioinformatic analysis of 279 putative GUS enzymes from the human gut microbiome and identified 12 additional putative GH2 GalAses, one of which we characterized and confirmed is a GalAse. Lastly, we report the structure of a hybrid GUS/GalAse from Fusicatenibacter saccharivorans, which revealed a unique hexamer that positions the N-terminus of adjacent protomers in the aglycone binding site. Taken together, these data reveal a new class of bacterial GalAses in the human gut microbiome and unravel the structural details that differentiate GH2 GUSs and GalAses.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galacturonidase
D, A, B, C
574Eisenbergiella tayiMutation(s): 0 
Gene Names: uidA_6
EC: 3.2.1.31
Find proteins for A0A1E3AEY6 (Eisenbergiella tayi)
Go to UniProtKB:  A0A1E3AEY6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ADA
Query on ADA

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-D-GALACTOPYRANURONIC ACID
ALPHA D-GALACTURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-BKBMJHBISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.342α = 90.00
b = 156.038β = 101.27
c = 124.285γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited States--

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection, Database references