Skip to main content

 3PHA | pdb_00003pha

The crystal structure of the W169Y mutant of alpha-glucosidase (gh31 family) from Ruminococcus obeum atcc 29174 in complex with acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.265 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3PHA

This is version 3.2 of the entry. See complete history. 

Literature

Interaction of antidiabetic alpha-glucosidase inhibitors and gut bacteria alpha-glucosidase.

Tan, K., Tesar, C., Wilton, R., Jedrzejczak, R.P., Joachimiak, A.

(2018) Protein Sci 27: 1498-1508

  • DOI: https://doi.org/10.1002/pro.3444
  • Primary Citation Related Structures: 
    3PHA, 3POC, 6C9X, 6C9Z, 6CA1, 6CA3

  • PubMed Abstract: 

    Carbohydrate hydrolyzing α-glucosidases are commonly found in microorganisms present in the human intestine microbiome. We have previously reported crystal structures of an α-glucosidase from the human gut bacterium Blaubia (Ruminococcus) obeum (Ro-αG1) and its substrate preference/specificity switch. This novel member of the GH31 family is a structural homolog of human intestinal maltase-glucoamylase (MGAM) and sucrase-isomaltase (SI) with a highly conserved active site that is predicted to be common in Ro-αG1 homologs among other species that colonize the human gut. In this report, we present structures of Ro-αG1 in complex with the antidiabetic α-glucosidase inhibitors voglibose, miglitol, and acarbose and supporting binding data. The in vitro binding of these antidiabetic drugs to Ro-αG1 suggests the potential for unintended in vivo crossreaction of the α-glucosidase inhibitors to bacterial α-glucosidases that are present in gut microorganism communities. Moreover, analysis of these drug-bound enzyme structures could benefit further antidiabetic drug development.


  • Organizational Affiliation: 
    • Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439.

Macromolecule Content 

  • Total Structure Weight: 312.29 kDa 
  • Atom Count: 22,569 
  • Modeled Residue Count: 2,660 
  • Deposited Residue Count: 2,664 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
alpha-glucosidase
A, B, C, D
666Blautia obeum ATCC 29174Mutation(s): 1 
Gene Names: RUMOBE_03919
EC: 3.2.1 (PDB Primary Data), 3.2.1.3 (UniProt)
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
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E, F, G, H
3N/AN/A
Glycosylation Resources
GlyTouCan: G66431MI
GlyCosmos: G66431MI

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.265 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.032α = 90
b = 125.955β = 107.72
c = 133.58γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2017-07-19
    Changes: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 3.2: 2026-09-30
    Changes: Database references, Structure summary