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

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/acs.biochem.8b01285
  • Primary Citation of Related Structures:  
    6NCW, 6NCX, 6NCY, 6NCZ

  • 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 (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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
574Eisenbergiella tayiMutation(s): 0 
Gene Names: uidA_6BEI59_03660BEI61_03198
Find proteins for A0A1E3AEY6 (Eisenbergiella tayi)
Explore A0A1E3AEY6 
Go to UniProtKB:  A0A1E3AEY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1E3AEY6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D]
C3 H8 O3
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
M [auth C],
P [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.93α = 93.29
b = 87.677β = 101.55
c = 124.375γ = 90.37
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references