3MKK

The crystal structure of the D307A mutant of glycoside HYDROLASE (FAMILY 31) from Ruminococcus obeum ATCC 29174 in complex with isomaltose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

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This is version 2.2 of the entry. See complete history


Literature

The Crystal Structures Of The Glycoside Hydrolase (Family 31) From Ruminococcus Obeum Atcc 29174

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alpha-glucosidase GH31 family
A, B
666Blautia obeum ATCC 29174Mutation(s): 1 
Gene Names: RUMOBE_03919
UniProt
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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G45624LJ
GlyCosmos:  G45624LJ
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download Ideal Coordinates CCD File 
E [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
GLC
Query on GLC

Download Ideal Coordinates CCD File 
D [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.449α = 90
b = 125.507β = 107.85
c = 87.867γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-06
    Changes: Advisory, Database references, Structure summary
  • Version 2.2: 2023-09-06
    Changes: Data collection, Refinement description