2INU | pdb_00002inu

Crystal structure of Inulin fructotransferase in the absence of substrate

• PDB DOI: https://doi.org/10.2210/pdb2INU/pdb

• Classification: LYASE
• Organism(s): Bacillus sp. snu-7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-09 Released: 2006-12-26 
• Deposition Author(s): Rhee, S., Jung, W.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.226 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.218 (DCC) 

Literature

Structural and functional insights into intramolecular fructosyl transfer by Inulin fructotransferase

Jung, W.S., Hong, C.K., Lee, S., Kim, C.S., Kim, S.J., Kim, S.I., Rhee, S.

(2007) J Biological Chem 282: 8414-8423

• PubMed: 17192265 
• DOI: https://doi.org/10.1074/jbc.M607143200
• Primary Citation Related Structures: 
  2INU, 2INV


• PubMed Abstract: 
  

  Inulin fructotransferase (IFTase), a member of glycoside hydrolase family 91, catalyzes depolymerization of beta-2,1-fructans inulin by successively removing the terminal difructosaccharide units as cyclic anhydrides via intramolecular fructosyl transfer. The crystal structures of IFTase and its substrate-bound complex reveal that IFTase is a trimeric enzyme, and each monomer folds into a right-handed parallel beta-helix. Despite variation in the number and conformation of its beta-strands, the IFTase beta-helix has a structure that is largely reminiscent of other beta-helix structures but is unprecedented in that trimerization is a prerequisite for catalytic activity, and the active site is located at the monomer-monomer interface. Results from crystallographic studies and site-directed mutagenesis provide a structural basis for the exolytic-type activity of IFTase and a functional resemblance to inverting-type glycosyltransferases.

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Organizational Affiliation: 
• Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.95 kDa 
• Atom Count: 9,530 
• Modeled Residue Count: 1,197 
• Deposited Residue Count: 1,230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inulin fructotransferase	A, B, C	410	Bacillus sp. snu-7	Mutation(s): 0  EC: 4.2.2.18
UniProt
Find proteins for Q3SAG3 (Bacillus sp. snu-7) Explore Q3SAG3  Go to UniProtKB:  Q3SAG3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PO	D [auth A], E [auth B]	PHOSPHONATE H O3 P ABLZXFCXXLZCGV-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.226 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.218 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.138	α = 90
b = 91.907	β = 124.75
c = 93.022	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-26 
Deposition Author(s): Rhee, S., Jung, W.S.

Revision History  

• Version 1.0: 2006-12-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-10-14
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Structure summary