3WKW

Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum ligand free form

Summary for 3WKW

• Entry DOI: 10.2210/pdb3wkw/pdb
• Related: 3WKX
• Descriptor: Non-reducing end beta-L-arabinofuranosidase (2 entities in total)
• Functional Keywords: (alpha/alpha)6 barrel, hydrolase, intracellular
• Biological source: Bifidobacterium longum
• Total number of polymer chains: 1
• Total formula weight: 74457.91

Authors

Ito, T.,Saikawa, K.,Arakawa, T.,Wakagi, T.,Fujita, K. (deposition date: 2013-11-01, release date: 2014-04-30, Last modification date: 2024-05-29)

Primary citation

Ito, T.,Saikawa, K.,Kim, S.,Fujita, K.,Ishiwata, A.,Kaeothip, S.,Arakawa, T.,Wakagi, T.,Beckham, G.T.,Ito, Y.,Fushinobu, S.
Crystal structure of glycoside hydrolase family 127 beta-l-arabinofuranosidase from Bifidobacterium longum.
Biochem.Biophys.Res.Commun., 447:32-37, 2014

PubMed Abstract: Enzymes acting on β-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of β-l-arabinofuranosyl oligosaccharides in plant cells. Recently, a β-l-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system of hydroxyproline-linked β-l-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and β-l-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional β-sandwich domains, with one β-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn(2+) coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the β-l-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.

PubMed: 24680821
DOI: 10.1016/j.bbrc.2014.03.096

Experimental method

X-RAY DIFFRACTION (2.2 Å)