3M46

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1096/fj.10-156257
  • Primary Citation of Related Structures:  

  • 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 wid ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, B
666Blautia obeum ATCC 29174Mutation(s): 1 
EC: 3.2.1.-
Find proteins for A5ZY13 (Blautia obeum ATCC 29174)
Go to UniProtKB:  A5ZY13
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
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: 2.66 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.182α = 90.00
b = 122.486β = 108.60
c = 87.460γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
MOLREPphasing
HKL-3000data reduction
SBC-Collectdata collection
HKL-3000phasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description