5ZYC

Crystal Structure of Glucose Isomerase Soaked with Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


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Literature

Structural analysis of substrate recognition by glucose isomerase in Mn2+binding mode at M2 site in S. rubiginosus

Bae, J.E.Hwang, K.Y.Nam, K.H.

(2018) Biochem Biophys Res Commun 503: 770-775

  • DOI: 10.1016/j.bbrc.2018.06.074
  • Primary Citation of Related Structures:  
    5ZYC, 5ZYD, 5ZYE

  • PubMed Abstract: 
  • Glucose isomerase (GI) catalyzes the reversible enzymatic isomerization of d-glucose and d-xylose to d-fructose and d-xylulose, respectively. This is one of the most important enzymes in the production of high-fructose corn syrup (HFCS) and biofuel. We recently determined the crystal structure of GI from S ...

    Glucose isomerase (GI) catalyzes the reversible enzymatic isomerization of d-glucose and d-xylose to d-fructose and d-xylulose, respectively. This is one of the most important enzymes in the production of high-fructose corn syrup (HFCS) and biofuel. We recently determined the crystal structure of GI from S. rubiginosus (SruGI) complexed with a xylitol inhibitor in one metal binding mode. Although we assessed inhibitor binding at the M1 site, the metal binding at the M2 site and the substrate recognition mechanism for SruGI remains the unclear. Here, we report the crystal structure of the two metal binding modes of SruGI and its complex with glucose. This study provides a snapshot of metal binding at the SruGI M2 site in the presence of Mn 2+ , but not in the presence of Mg 2+ . Metal binding at the M2 site elicits a configuration change at the M1 site. Glucose molecule can only bind to the M1 site in presence of Mn 2+ at the M2 site. Glucose and Mn 2+ at the M2 site were bridged by water molecules using a hydrogen bonding network. The metal binding geometry of the M2 site indicates a distorted octahedral coordination with an angle of 55-110°, whereas the M1 site has a relatively stable octahedral coordination with an angle of 85-95°. We suggest a two-step sequential process for SruGI substrate recognition, in Mn 2+ binding mode, at the M2 site. Our results provide a better understanding of the molecular role of the M2 site in GI substrate recognition.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea. Electronic address: structures@korea.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xylose isomeraseA388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.456α = 90
b = 97.921β = 90
c = 101.988γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-05-24 
  • Released Date: 2018-11-28 
  • Deposition Author(s): Nam, K.H.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1D1A1B03033087
National Research Foundation (Korea)Korea, Republic Of2017M3A9F6029736

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release