8XVQ | pdb_00008xvq

Crystal structure of inulosucrase from Lactobacillus reuteri 121 in complex with fructose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structure-Guided Tunnel Engineering to Reveal the Molecular Basis of Sugar Chain Extension of Inulosucrase.

Ni, D.Huang, Z.Zhang, S.Hou, X.Xu, W.Zhang, W.Rao, Y.Mu, W.

(2025) J Agric Food Chem 73: 16454-16467

  • DOI: https://doi.org/10.1021/acs.jafc.5c02217
  • Primary Citation Related Structures: 
    8XVP, 8XVQ, 8XVR

  • PubMed Abstract: 

    Inulosucrase (IS) is a key enzyme in the synthesis of inulin, a multifunctional polysaccharide with significant physiological benefits and wide-ranging applications. Lactobacillus IS has the unique capability to produce both high-molecular-weight polysaccharides and oligosaccharides with diverse degrees of polymerization. Understanding the mechanism of sugar chain extension by IS is essential for modulating chain length and engineering custom-designed inulin. In this study, we resolved the crystal structures of IS from Lactobacillus reuteri 121 and its mutant IS-R544W, revealing a unique C-terminal extension into the catalytic pocket. Notably, structure-guided rational design identified IS-Tyr695 in the C-terminal region, along with IS-Asn303, IS-Asn305, IS-Asn367, IS-Gln369, and IS-Asn419, as critical residues specifically required for polysaccharide synthesis without affecting oligosaccharide production. In contrast, IS-Arg544, IS-Tyr618, and IS-Arg622 were determined to be essential for oligosaccharide synthesis with no impact on polysaccharide production. Based on findings from rational design and molecular dynamics simulations, we propose a novel shunting mechanism for the synthesis of polysaccharides and oligosaccharides by IS. This study provides fundamental insights into the inulin chain extension mechanism of IS and lays a theoretical foundation for engineering GH68 enzymes for the production of tailor-made fructans.


  • Organizational Affiliation
    • State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China.

Macromolecule Content 

  • Total Structure Weight: 174.07 kDa 
  • Atom Count: 8,483 
  • Modeled Residue Count: 1,036 
  • Deposited Residue Count: 1,596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inulosucrase
A, B
798Limosilactobacillus reuteriMutation(s): 0 
Gene Names: inuDPH67_05265
EC: 2.4.1.9
UniProt
Find proteins for Q8GP32 (Limosilactobacillus reuteri)
Explore Q8GP32 
Go to UniProtKB:  Q8GP32
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GP32
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.24α = 90
b = 99.92β = 90
c = 153.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateChina2023YFF1103600
National Natural Science Foundation of China (NSFC)China22308118
Other privateChinaBK20231045

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references