8XVR | pdb_00008xvr

Crystal structure of inulosucrase from Lactobacillus reuteri 121 mutant R544W


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 
    0.216 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8XVR

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: 263.56 kDa 
  • Atom Count: 17,513 
  • Modeled Residue Count: 2,083 
  • Deposited Residue Count: 2,352 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 68 protein
A, B, C, D
588Limosilactobacillus reuteriMutation(s): 1 
Gene Names: DPAN417_05420
UniProt
Find proteins for A0A7X2FZN4 (Limosilactobacillus reuteri)
Explore A0A7X2FZN4 
Go to UniProtKB:  A0A7X2FZN4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7X2FZN4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
(Subject of Investigation/LOI)

Query on 1PE



Download:Ideal Coordinates CCD File
M [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PEG
(Subject of Investigation/LOI)

Query on PEG



Download:Ideal Coordinates CCD File
QA [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
(Subject of Investigation/LOI)

Query on GOL



Download:Ideal Coordinates CCD File
HA [auth C],
IA [auth C],
L [auth A],
PA [auth D],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
LA [auth D],
MA [auth D],
NA [auth D],
OA [auth D],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
JA [auth D]
KA [auth D]
N [auth B]
E [auth A],
F [auth A],
JA [auth D],
KA [auth D],
N [auth B],
O [auth B],
X [auth C],
Y [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free:  0.216 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.57α = 90
b = 132.08β = 110.29
c = 121.78γ = 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 private2023YFF1103600
National Natural Science Foundation of China (NSFC)China22308118
Other privateBK20231045

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