9J4L

Crystal structure of GH9l Inulin fructotransferases (IFTase)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Elucidation of the mechanism underlying the sequential catalysis of inulin by fructotransferase.

Chen, G.Wang, Z.X.Yang, Y.Li, Y.Zhang, T.Ouyang, S.Zhang, L.Chen, Y.Ruan, X.Miao, M.

(2024) Int J Biol Macromol 277: 134446-134446

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.134446
  • Primary Citation of Related Structures:  
    9J4I, 9J4J, 9J4K, 9J4L

  • PubMed Abstract: 

    Glycoside hydrolase family 91 (GH91) inulin fructotransferase (IFTases) enables biotransformation of fructans into sugar substitutes for dietary intervention in metabolic syndrome. However, the catalytic mechanism underlying the sequential biodegradation of inulin remains unelusive during the biotranformation of fructans. Herein we present the crystal structures of IFTase from Arthrobacter aurescens SK 8.001 in apo form and in complexes with kestose, nystose, or fructosyl nystose, respectively. Two kinds of conserved noncatalytic binding regions are first identified for IFTase-inulin interactions. The conserved interactions of substrates were revealed in the catalytic center that only contained a catalytic residue E205. A switching scaffold was comprised of D194 and Q217 in the catalytic channel, which served as the catalytic transition stabilizer through side chain displacement in the cycling of substrate sliding in/out the catalytic pocket. Such features in GH91 contribute to the catalytic model for consecutive cutting of substrate chain as well as product release in IFTase, and thus might be extended to other exo-active enzymes with an enclosed bottom of catalytic pocket. The study expands the current general catalytic principle in enzyme-substrate complexes and shed light on the rational design of IFTase for fructan biotransformation.


  • Organizational Affiliation

    State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou 311300, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DFA-III-forming inulin fructotransferase
A, B, C
404Paenarthrobacter aurescensMutation(s): 0 
Gene Names: ift
EC: 4.2.2.18
UniProt
Find proteins for F8QV43 (Paenarthrobacter aurescens)
Explore F8QV43 
Go to UniProtKB:  F8QV43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8QV43
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.68α = 90
b = 167.68β = 90
c = 85.66γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
RESOLVEmodel building
HKL-3000data scaling
HKL-3000data reduction
RESOLVEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina2018YFC1602101
National Natural Science Foundation of China (NSFC)China31972029
National Natural Science Foundation of China (NSFC)China31770948

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-09-18
    Changes: Database references