Crystal Structures of Decorated Xylooligosaccharides Bound to a Family 10 Xylanase from Streptomyces olivaceoviridis E-86

Abstract

The family 10 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn10A) consists of a GH10 catalytic domain, which is joined by a Gly/Pro-rich linker to a family 13 carbohydrate-binding module (CBM13) that interacts with xylan. To understand how GH10 xylanases and CBM13 recognize decorated xylans, the crystal structure of SoXyn10A was determined in complex with ␣-L- CBM13 was shown to bind xylose or xylooligosaccharides reversibly by using nonsymmetric sugars as the ligands. The independent multiple sites in CBM13 may increase the probability of substrate binding.

The Mechanisms by Which Family 10 Glycoside Hydrolases Bind Decorated Substrates

“…5a) was refined to a final R-factor of 0.16 and R free of 0.20. The 4-O-MeGlcA of the decorated xylooligosaccharide is accommodated in the ϩ1 subsite, which is entirely consistent with the biochemical properties of not only CmXyn10B but other GH10 xylanases, including SoXyn10A described in the accompanying paper (19), as MX 3 is the major substituted product generated from glucuronoxylan by these enzymes (16). No 4-O-MeGlcA can be modeled in the Ϫ3 subsite, as the electron density is diffuse; this is consistent with the observation that it does not interact with the enzyme but is simply accommodated (the O-2 of the xylose moiety at this location is solvent-exposed).…”

“…No 4-O-MeGlcA can be modeled in the Ϫ3 subsite, as the electron density is diffuse; this is consistent with the observation that it does not interact with the enzyme but is simply accommodated (the O-2 of the xylose moiety at this location is solvent-exposed). It is interesting to note, however, that although the uronic acid also does not interact with the Ϫ3 subsite of SoXyn10A, clear electron density for 4-OMeGlcA is evident at this subsite (19). In CmXyn10B the electron density of 4-O-MeGlcA at the ϩ1 subsite is clearly defined, indicating that the side chain has a more restricted conformation because of direct interactions with the aglycone region of the active site (Fig.…”

“…At the ϩ4 subsite the O-3 of the xylose residue interacts only with the side chain of Ser-270. The variation in substrate recognition in the distal region of the aglycone binding cleft of GH10 xylanases, alluded to above, is further illustrated by the accompanying paper (19), which demonstrates a lack of substrate binding at the ϩ3 subsite of SoXyn10A. The structure of CmXyn10B in complex with xylopentaose bound to both the glycone and aglycone region of the substrate binding cleft provides the first glimpses of the conformation of xylan when bound to all subsites of a GH10 xylanase.…”

“…Its capacity to bind decorated substrates is conferred partly by the exposure of O-2 and O-3 groups at selected glycone and aglycone subsites and partly through productive interactions with the 4-OMeGlcA side chains. The data provided here and in the accompanying paper by Fujimoto et al (19) focus on a GH10 xylanase that contains an N-terminal lectin domain (19), reveal complementarity in the binding of decorated substrates between the glycone and aglycone regions of the active site, and demonstrate how these binding modes mediate synergy with the xylan accessory enzyme, ␣-glucuronidase.…”

Crystal Structure of a Family 54 α-l-Arabinofuranosidase Reveals a Novel Carbohydrate-binding Module That Can Bind Arabinose

“…Recently, the crystal structures of CBMs complexed with oligosaccharides decorated with side-chain sugars have been reported. The crystal structures of S. olivaceoviridis CBM13 in complexes with ␣-L-arabinofuranosyl-and 4-O-methyl-␣-D-glucuronosyl-xylooligosaccharides have been determined (47). The sugar-binding site in CBM13 interacts mainly with a single xylose moiety of the xylooligosaccharides.…”