3WN1

Crystal Structure of Streptomyces coelicolor alpha-L-arabinofuranosidase in complex with xylotriose

Summary for 3WN1

• Entry DOI: 10.2210/pdb3wn1/pdb
• Related: 3WMY 3WMZ 3WN0 3WN2
• Related PRD ID: PRD_900117
• Descriptor: Extracellular exo-alpha-L-arabinofuranosidase, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose, CALCIUM ION, ... (7 entities in total)
• Functional Keywords: five-bladed beta-propeller, glycoside hydrolase, hydrolase
• Biological source: Streptomyces coelicolor
• Cellular location: Secreted : O54161
• Total number of polymer chains: 1
• Total formula weight: 47520.35

Authors

Fujimoto, Z.,Maehara, T.,Ichinose, H.,Michikawa, M.,Harazono, K.,Kaneko, S. (deposition date: 2013-11-29, release date: 2014-02-05, Last modification date: 2023-11-08)

Primary citation

Maehara, T.,Fujimoto, Z.,Ichinose, H.,Michikawa, M.,Harazono, K.,Kaneko, S.
Crystal structure and characterization of the glycoside hydrolase family 62 alpha-L-arabinofuranosidase from Streptomyces coelicolor
J.Biol.Chem., 289:7962-7972, 2014

PubMed Abstract: α-L-arabinofuranosidase, which belongs to the glycoside hydrolase family 62 (GH62), hydrolyzes arabinoxylan but not arabinan or arabinogalactan. The crystal structures of several α-L-arabinofuranosidases have been determined, although the structures, catalytic mechanisms, and substrate specificities of GH62 enzymes remain unclear. To evaluate the substrate specificity of a GH62 enzyme, we determined the crystal structure of α-L-arabinofuranosidase, which comprises a carbohydrate-binding module family 13 domain at its N terminus and a catalytic domain at its C terminus, from Streptomyces coelicolor. The catalytic domain was a five-bladed β-propeller consisting of five radially oriented anti-parallel β-sheets. Sugar complex structures with l-arabinose, xylotriose, and xylohexaose revealed five subsites in the catalytic cleft and an l-arabinose-binding pocket at the bottom of the cleft. The entire structure of this GH62 family enzyme was very similar to that of glycoside hydrolase 43 family enzymes, and the catalytically important acidic residues found in family 43 enzymes were conserved in GH62. Mutagenesis studies revealed that Asp(202) and Glu(361) were catalytic residues, and Trp(270), Tyr(461), and Asn(462) were involved in the substrate-binding site for discriminating the substrate structures. In particular, hydrogen bonding between Asn(462) and xylose at the nonreducing end subsite +2 was important for the higher activity of substituted arabinofuranosyl residues than that for terminal arabinofuranoses.

PubMed: 24482228
DOI: 10.1074/jbc.M113.540542

Experimental method

X-RAY DIFFRACTION (2 Å)