2YFT

Crystal structure of inulosucrase from Lactobacillus johnsonii NCC533 in complex with 1-kestose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Inulosucrase from Lactobacillus: Insights Into the Substrate Specificity and Product Specificity of Gh68 Fructansucrases.

Pijning, T.Anwar, M.A.Boger, M.Dobruchowska, J.M.Leemhuis, H.Kralj, S.Dijkhuizen, L.Dijkstra, B.W.

(2011) J.Mol.Biol. 412: 80

  • DOI: 10.1016/j.jmb.2011.07.031
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fructansucrases (FSs) catalyze a transfructosylation reaction with sucrose as substrate to produce fructo-oligosaccharides and fructan polymers that contain either β-2,1 glycosidic linkages (inulin) or β-2,6 linkages (levan). Levan-synthesizing FSs ( ...

    Fructansucrases (FSs) catalyze a transfructosylation reaction with sucrose as substrate to produce fructo-oligosaccharides and fructan polymers that contain either β-2,1 glycosidic linkages (inulin) or β-2,6 linkages (levan). Levan-synthesizing FSs (levansucrases) have been most extensively investigated, while detailed information on inulosucrases is limited. Importantly, the molecular basis of the different product specificities of levansucrases and inulosucrases is poorly understood. We have elucidated the three-dimensional structure of a truncated active bacterial GH68 inulosucrase, InuJ of Lactobacillus johnsonii NCC533 (residues 145-708), in its apo form, with a bound substrate (sucrose), and with a transfructosylation product. The sucrose binding pocket and the sucrose binding mode are virtually identical with those of GH68 levansucrases, confirming that both enzyme types use the same fully conserved structural framework for the binding and cleavage of the donor substrate sucrose in the active site. The binding mode of the first transfructosylation product 1-kestose (Fru-β(2-1)-Fru-α(2-1)-Glc, where Fru=fructose and Glc=glucose) in subsites -1 to +2 shows for the first time how inulin-type fructo-oligosaccharide bind in GH68 FS and how an inulin-type linkage can be formed. Surprisingly, observed interactions with the sugar in subsites +1 and +2 are provided by residues that are also present in levansucrases. The binding mode of 1-kestose and the presence of a more distant sucrose binding site suggest that residues beyond the +2 subsite, in particular residues from the nonconserved 1B-1C loop, determine product linkage type specificity in GH68 FSs.


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEVANSUCRASE
A
571Lactobacillus johnsonii (strain CNCM I-12250 / La1 / NCC 533)Mutation(s): 0 
Gene Names: inuJ (ftf)
EC: 2.4.1.9
Find proteins for Q74K42 (Lactobacillus johnsonii (strain CNCM I-12250 / La1 / NCC 533))
Go to UniProtKB:  Q74K42
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DQR
Query on DQR

Download SDF File 
Download CCD File 
A
beta-D-fructofuranosyl-(2->1)-beta-D-fructofuranosyl alpha-D-glucopyranoside
1-KESTOSE
C18 H32 O16
VAWYEUIPHLMNNF-OESPXIITSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 171.204α = 90.00
b = 171.204β = 90.00
c = 115.003γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2011-08-17
    Type: Non-polymer description
  • Version 1.2: 2011-08-31
    Type: Database references
  • Version 1.3: 2014-06-11
    Type: Refinement description