Crystal Structure of Levan Fructotransferase D54N mutant from Arthrobacter ureafaciens in complex with sucrose

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 

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This is version 2.1 of the entry. See complete history


Structural and functional basis for substrate specificity and catalysis of levan fructotransferase.

Park, J.Kim, M.I.Park, Y.D.Shin, I.Cha, J.Kim, C.H.Rhee, S.

(2012) J Biol Chem 287: 31233-31241

  • DOI: https://doi.org/10.1074/jbc.M112.389270
  • Primary Citation of Related Structures:  
    4FFF, 4FFG, 4FFH, 4FFI

  • PubMed Abstract: 

    Levan is β-2,6-linked polymeric fructose and serves as reserve carbohydrate in some plants and microorganisms. Mobilization of fructose is usually mediated by enzymes such as glycoside hydrolase (GH), typically releasing a monosaccharide as a product. The enzyme levan fructotransferase (LFTase) of the GH32 family catalyzes an intramolecular fructosyl transfer reaction and results in production of cyclic difructose dianhydride, thus exhibiting a novel substrate specificity. The mechanism by which LFTase carries out these functions via the structural fold conserved in the GH32 family is unknown. Here, we report the crystal structure of LFTase from Arthrobacter ureafaciens in apo form, as well as in complexes with sucrose and levanbiose, a difructosacchride with a β-2,6-glycosidic linkage. Despite the similarity of its two-domain structure to members of the GH32 family, LFTase contains an active site that accommodates a difructosaccharide using the -1 and -2 subsites. This feature is unique among GH32 proteins and is facilitated by small side chain residues in the loop region of a catalytic β-propeller N-domain, which is conserved in the LFTase family. An additional oligosaccharide-binding site was also characterized in the β-sandwich C-domain, supporting its role in carbohydrate recognition. Together with functional analysis, our data provide a molecular basis for the catalytic mechanism of LFTase and suggest functional variations from other GH32 family proteins, notwithstanding the conserved structural elements.

  • Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Levan fructotransferase
A, B, C, D
492Paenarthrobacter ureafaciensMutation(s): 1 
Gene Names: lftA
Find proteins for Q9KJD0 (Paenarthrobacter ureafaciens)
Explore Q9KJD0 
Go to UniProtKB:  Q9KJD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KJD0
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, F, G, H, I
E, F, G, H, I, J
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.284α = 90
b = 167.004β = 90
c = 261.926γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Database references
  • Version 1.2: 2012-09-26
    Changes: Database references
  • Version 1.3: 2017-05-10
    Changes: Non-polymer description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references, Structure summary