8WDG

Subatomic crystal structure of glucose isomerase from Streptomyces rubiginosus

  • Classification: ISOMERASE
  • Organism(s): Streptomyces rubiginosus
  • Mutation(s): No 

  • Deposited: 2023-09-15 Released: 2023-10-04 
  • Deposition Author(s): Nam, K.H.
  • Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

Starting Model: experimental
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Literature

Xylitol binding to the M1 site of glucose isomerase induces a conformational change in the substrate binding channel.

Xu, Y.Nam, K.H.

(2023) Biochem Biophys Res Commun 682: 21-26

  • DOI: https://doi.org/10.1016/j.bbrc.2023.09.087
  • Primary Citation of Related Structures:  
    8WDG

  • PubMed Abstract: 

    Glucose isomerase (GI) is extensively used in the food industry for production of high-fructose corn syrup and for the production of biofuels and other renewable chemicals. Structure-based studies on GI inhibitors are important for improving its efficiency in industrial applications. Here, we report the subatomic crystal structure of Streptomyces rubiginosus GI (SruGI) complexed with its inhibitor, xylitol, at 0.99 Å resolution. Electron density map and temperature factor analysis showed partial binding of xylitol to the M1 metal binding site of SruGI, providing two different conformations of the metal binding site and the substrate binding channel. The xylitol molecule induced a conformational change in the M2 metal ion-interacting Asp255 residue, which subsequently led to a conformational change in the side chain of Asp181 residue. This led to the positional shift of Pro25 by 1.71 Å and side chain rotation of Phe26 by 21°, where located on the neighboring protomer in tetrameric SruGI. The conformation change of these two residues affect the size of the substrate-binding channel of GI. Therefore, xylitol binding to M1 site of SruGI induces not only a conformational changes of the metal-binding site, but also conformational change of substrate-binding channel of the tetrameric SruGI. These results expand our knowledge about the mechanism underlying the inhibitory effect of xylitol on GI.


  • Organizational Affiliation

    Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, China; Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian, 116600, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase385Streptomyces rubiginosusMutation(s): 0 
EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24300
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.675α = 90
b = 98.626β = 90
c = 102.137γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2023-10-04 
  • Deposition Author(s): Nam, K.H.

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021R1I1A1A01050838
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2017M3A9F6029736
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2020M3H1A1075314

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references