Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module

Fujimoto, Zui; Kuno, Atsushi; Kaneko, Satoshi; Kobayashi, Hideyuki; Kusakabe, Isao; Mizuno, Hiroshi

doi:10.1006/jmbi.2001.5338

Cited by 82 publications

(67 citation statements)

References 44 publications

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“…Further binding studies of CBM13 show that the protein prefers highly polymeric ligands, although it displays broad specificity for several mono-and disaccharides. These biochemical studies are supported by the crystal structure of mature SoXyn10A in complex with a variety of ligands (18,19). These data show that * This work was performed with the support of the Photon Factory, High Energy Accelerator Research Organization, Japan (Proposal 2000G294).…”

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confidence: 79%

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

Fujimoto

Kaneko

Kuno

et al. 2004

Journal of Biological Chemistry

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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.

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confidence: 79%

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

Fujimoto

Kaneko

Kuno

et al. 2004

Journal of Biological Chemistry

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“…Homology models of the first two domains and the C-terminal carbohydrate-binding module family 13 (CBM13) of SaArap27A were built with the MODELER program (Accelrys Software Inc., San Diego, CA) using the known crystal structures of rice ␣-galactosidase and CBM13 of Streptomyces olivaceoviridis ␤-xylanase (SoCBM13), respectively, as reference models (25,26). The first run of the MOLREP program (27) in the CCP4 program suite (28) using the ␣-galactosidase-derived model as the reference against the native data resulted in two prominent solutions yielding an R factor of 0.553.…”

Section: Methodsmentioning

confidence: 99%

A β-l-Arabinopyranosidase from Streptomyces avermitilis Is a Novel Member of Glycoside Hydrolase Family 27

Ichinose

Fujimoto

Honda

et al. 2009

Journal of Biological Chemistry

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Arabinogalactan proteins (AGPs) are a family of plant cell surface proteoglycans and are considered to be involved in plant growth and development. Because AGPs are very complex molecules, glycoside hydrolases capable of degrading AGPs are powerful tools for analyses of the AGPs. We previously reported such enzymes from Streptomyces avermitilis. Recently, a ␤-Larabinopyranosidase was purified from the culture supernatant of the bacterium, and its corresponding gene was identified. The primary structure of the protein revealed that the catalytic module was highly similar to that of glycoside hydrolase family 27 (GH27) ␣-D-galactosidases. The recombinant protein was successfully expressed as a secreted 64-kDa protein using a Streptomyces expression system. The specific activity toward p-nitrophenyl-␤-L-arabinopyranoside was 18 mol of arabinose/min/mg, which was 67 times higher than that toward pnitrophenyl-␣-D-galactopyranoside. The enzyme could remove 0.1 and 45% L-arabinose from gum arabic or larch arabinogalactan, respectively. X-ray crystallographic analysis reveals that the protein had a GH27 catalytic domain, an antiparallel ␤-domain containing Greek key motifs, another antiparallel ␤-domain forming a jellyroll structure, and a carbohydrate-binding module family 13 domain. Comparison of the structure of this protein with that of ␣-D-galactosidase showed a single amino acid substitution (aspartic acid to glutamic acid) in the catalytic pocket of ␤-L-arabinopyranosidase, and a space for the hydroxymethyl group on the C-5 carbon of D-galactose bound to ␣-galactosidase was changed in ␤-L-arabinopyranosidase. Mutagenesis study revealed that the residue is critical for modulating the enzyme activity. This is the first report in which ␤-L-arabinopyranosidase is classified as a new member of the GH27 family.Arabinogalactan proteins (AGPs) 3 are a family of complex proteoglycans widely distributed in plants (1, 2). AGPs are also found in tree exudate gums and coniferous woods (3) and are characterized by the presence of large amounts of carbohydrate components rich in galactose (all the sugars in the present study are in the D-configuration unless otherwise specified) and L-arabinose and by protein components rich in hydroxyproline, serine, threonine, alanine, and glycine (4). Type II arabinogalactans and short oligosaccharides are the two types of carbohydrates attached to the AGP backbone. Type II arabinogalactans have ␤-1,3-linked galactosyl backbones in mono-or oligo-␤-1,6-galactosyl and/or L-arabinosyl side chains (2, 5). L-Arabinose and lesser amounts of other auxiliary sugars such as glucuronic acid, L-rhamnose, and L-fucose are attached to the side chains primarily at nonreducing termini (2). Molecular and biochemical evidence indicates that AGPs have specific functions during root formation, promotion of somatic embryogenesis, and attraction of pollen tubes to the style (6). However, because many putative protein cores exist and the structures of the carbohydrate moieties are complex, it has been difficult...

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“…The fold of the resulting molecule has a pseudo-3-fold axis [45,46]. The 3-fold symmetry is amenable to the presence of functional carbohydrate-binding sites in each of the three trefoil subdomains, which is exploited by the CBM13 modules of Streptomyces lividans and Streptomyces olivaceoviridis xylanases in order to maintain a reasonably high affinity for β-1,4-linked polymers of xylose [47][48][49][50]. The plant lectins with this fold, e.g.…”

Section: The β-Trefoilmentioning

confidence: 99%

Carbohydrate-binding modules: fine-tuning polysaccharide recognition

Boraston

Bolam

Gilbert

et al. 2004

Biochemical Journal

1,780

1,724

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The enzymic degradation of insoluble polysaccharides is one of the most important reactions on earth. Despite this, glycoside hydrolases attack such polysaccharides relatively inefficiently as their target glycosidic bonds are often inaccessible to the active site of the appropriate enzymes. In order to overcome these problems, many of the glycoside hydrolases that utilize insoluble substrates are modular, comprising catalytic modules appended to one or more non-catalytic CBMs (carbohydrate-binding modules). CBMs promote the association of the enzyme with the substrate. In view of the central role that CBMs play in the enzymic hydrolysis of plant structural and storage polysaccharides, the ligand specificity displayed by these protein modules and the mechanism by which they recognize their target carbohydrates have received considerable attention since their discovery almost 20 years ago. In the last few years, CBM research has harnessed structural, functional and bioinformatic approaches to elucidate the molecular determinants that drive CBM-carbohydrate recognition. The present review summarizes the impact structural biology has had on our understanding of the mechanisms by which CBMs bind to their target ligands.

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Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module

Cited by 82 publications

References 44 publications

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

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

A β-l-Arabinopyranosidase from Streptomyces avermitilis Is a Novel Member of Glycoside Hydrolase Family 27

Carbohydrate-binding modules: fine-tuning polysaccharide recognition

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