7V1W

Difructose dianhydride I synthase/hydrolase (alphaFFase1) from Bifidobacterium dentium in complex with beta-D-arabinofuranose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family.

Kashima, T.Okumura, K.Ishiwata, A.Kaieda, M.Terada, T.Arakawa, T.Yamada, C.Shimizu, K.Tanaka, K.Kitaoka, M.Ito, Y.Fujita, K.Fushinobu, S.

(2021) J Biol Chem 297: 101324-101324

  • DOI: https://doi.org/10.1016/j.jbc.2021.101324
  • Primary Citation of Related Structures:  
    7V1V, 7V1W, 7V1X

  • PubMed Abstract: 

    Fructooligosaccharides and their anhydrides are widely used as health-promoting foods and prebiotics. Various enzymes acting on β-D-fructofuranosyl linkages of natural fructan polymers have been used to produce functional compounds. However, enzymes that hydrolyze and form α-D-fructofuranosyl linkages have been less studied. Here, we identified the BBDE_2040 gene product from Bifidobacterium dentium (α-D-fructofuranosidase and difructose dianhydride I synthase/hydrolase from Bifidobacterium dentium [αFFase1]) as an enzyme with α-D-fructofuranosidase and α-D-arabinofuranosidase activities and an anomer-retaining manner. αFFase1 is not homologous with any known enzymes, suggesting that it is a member of a novel glycoside hydrolase family. When caramelized fructose sugar was incubated with αFFase1, conversions of β-D-Frup-(2→1)-α-D-Fruf to α-D-Fruf-1,2':2,1'-β-D-Frup (diheterolevulosan II) and β-D-Fruf-(2→1)-α-D-Fruf (inulobiose) to α-D-Fruf-1,2':2,1'-β-D-Fruf (difructose dianhydride I [DFA I]) were observed. The reaction equilibrium between inulobiose and DFA I was biased toward the latter (1:9) to promote the intramolecular dehydrating condensation reaction. Thus, we named this enzyme DFA I synthase/hydrolase. The crystal structures of αFFase1 in complex with β-D-Fruf and β-D-Araf were determined at the resolutions of up to 1.76 Å. Modeling of a DFA I molecule in the active site and mutational analysis also identified critical residues for catalysis and substrate binding. The hexameric structure of αFFase1 revealed the connection of the catalytic pocket to a large internal cavity via a channel. Molecular dynamics analysis implied stable binding of DFA I and inulobiose to the active site with surrounding water molecules. Taken together, these results establish DFA I synthase/hydrolase as a member of a new glycoside hydrolase family (GH172).


  • Organizational Affiliation

    Department of Biotechnology, The University of Tokyo, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Difructose dianhydride I synthase/hydrolase (alphaFFase1)
A, B, C, D, E
A, B, C, D, E, F
460Bifidobacterium dentiumMutation(s): 0 
Gene Names: BDLFYP24_02130
UniProt
Find proteins for A0A6L9SN29 (Bifidobacterium dentium)
Explore A0A6L9SN29 
Go to UniProtKB:  A0A6L9SN29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6L9SN29
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BXX (Subject of Investigation/LOI)
Query on BXX

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
Q [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
Q [auth E],
R [auth F]
beta-D-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-SQOUGZDYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth D]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth D],
P [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.451α = 90
b = 156.707β = 110.66
c = 100.849γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MoRDaphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan26660083
Japan Society for the Promotion of Science (JSPS)Japan24380053

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 2.0: 2022-01-12
    Type: Coordinate replacement
    Reason: Atoms with unrealistic or zero occupancies
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2022-02-16
    Changes: Database references
  • Version 2.2: 2023-11-29
    Changes: Data collection, Refinement description