The crystal structure of the D73A mutant of glycoside HYDROLASE (FAMILY 31) from Ruminococcus obeum ATCC 29174

Experimental Data Snapshot

  • Resolution: 2.66 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Novel alpha-glucosidase from human gut microbiome: substrate specificities and their switch

Tan, K.Tesar, C.Wilton, R.Keigher, L.Babnigg, G.Joachimiak, A.

(2010) FASEB J 24: 3939-3949

  • DOI: https://doi.org/10.1096/fj.10-156257
  • Primary Citation of Related Structures:  
    3M46, 3M6D, 3MKK, 3N04

  • PubMed Abstract: 

    The human intestine harbors a large number of microbes forming a complex microbial community that greatly affects the physiology and pathology of the host. In the human gut microbiome, the enrichment in certain protein gene families appears to be widespread. They include enzymes involved in carbohydrate metabolism such as glucoside hydrolases of dietary polysaccharides and glycoconjugates. We report the crystal structures (wild type, 2 mutants, and a mutant/substrate complex) and the enzymatic activity of a recombinant α-glucosidase from human gut bacterium Ruminococcus obeum. The first ever protein structures from this bacterium reveal a structural homologue to human intestinal maltase-glucoamylase with a highly conserved catalytic domain and reduced auxiliary domains. The α-glucosidase, a member of GH31 family, shows substrate preference for α(1-6) over α(1-4) glycosidic linkages and produces glucose from isomaltose as well as maltose. The preference can be switched by a single mutation at its active site, suggestive of widespread adaptation to utilization of a variety of polysaccharides by intestinal micro-organisms as energy resources.

  • Organizational Affiliation

    Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
666Blautia obeum ATCC 29174Mutation(s): 1 
Gene Names: RUMOBE_03919
Find proteins for A5ZY13 (Blautia obeum ATCC 29174)
Explore A5ZY13 
Go to UniProtKB:  A5ZY13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5ZY13
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.66 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.182α = 90
b = 122.486β = 108.6
c = 87.46γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2021-10-06
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description