7V1V

Difructose dianhydride I synthase/hydrolase (alphaFFase1) from Bifidobacterium dentium, ligand-free form

Summary for 7V1V

• Entry DOI: 10.2210/pdb7v1v/pdb
• Descriptor: Difructose dianhydride I synthase/hydrolase (alphaFFase1), CALCIUM ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total)
• Functional Keywords: glycoside hydrolase, alpha-d-fructofuranosidase, ligand-free, hydrolase
• Biological source: Bifidobacterium dentium
• Total number of polymer chains: 6
• Total formula weight: 319047.15

Authors

Kashima, T.,Arakawa, T.,Yamada, C.,Fujita, K.,Fushinobu, S. (deposition date: 2021-08-06, release date: 2021-11-03, Last modification date: 2023-11-29)

Primary citation

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.
Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family.
J.Biol.Chem., 297:101324-101324, 2021

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).

PubMed: 34688653
DOI: 10.1016/j.jbc.2021.101324

Experimental method

X-RAY DIFFRACTION (1.96 Å)