Crystal structures of glycoside hydrolase family 51 α-L- arabinofuranosidase from Thermotoga maritima

Do Hyun Im; Kei Ichi Kimura; Fumitaka Hayasaka; Tomonari Tanaka; Masato Noguchi; Atsushi Kobayashi; Shin Ichiro Shoda; Kentaro Miyazaki; Takayoshi Wakagi; Shinya Fushinobu

doi:10.1271/bbb.110902

Crystal structures of glycoside hydrolase family 51 α-L- arabinofuranosidase from Thermotoga maritima

Do Hyun Im, Kei Ichi Kimura, Fumitaka Hayasaka, Tomonari Tanaka, Masato Noguchi, Atsushi Kobayashi, Shin Ichiro Shoda, Kentaro Miyazaki, Takayoshi Wakagi, Shinya Fushinobu

Research output: Contribution to journal › Article › peer-review

12 Citations (Scopus)

Abstract

α-L-Arabinofuranosidase from the hyperthermophilic bacterium Thermotoga maritima (Tm-AFase) is an extremely thermophilic enzyme belonging to glycoside hydrolase family 51. It can catalyze the transglycosylation of a novel glycosyl donor, 4,6-dimethoxy-1,3,5-triazin-2-yl (DMT)-β-D-xylopyranoside. In this study we determined the crystal structures of Tm-AFase in substrate-free and complex forms with arabinose and xylose at 1.8-2.3Å resolution to determine the architecture of the substrate binding pocket. Subsite α1 of Tm-AFase is similar to that of α-L-arabinofuranosidase from Geobacillus stearothermophilus, but the substrate binding pocket of Tm-AFase is narrower and more hydrophobic. Possible substrate binding modes were investigated by automated docking analysis.

Original language	English
Pages (from-to)	423-428
Number of pages	6
Journal	Bioscience, Biotechnology and Biochemistry
Volume	76
Issue number	2
DOIs	https://doi.org/10.1271/bbb.110902
Publication status	Published - 2012
Externally published	Yes

Keywords

Arabinose
Glycoside hydrolase family 51
Thermotoga maritima
Xylose
α-L-arabinofuranosidase

ASJC Scopus subject areas

Biotechnology
Analytical Chemistry
Biochemistry
Applied Microbiology and Biotechnology
Molecular Biology
Organic Chemistry

Access to Document

10.1271/bbb.110902

Fingerprint Dive into the research topics of 'Crystal structures of glycoside hydrolase family 51 α-L- arabinofuranosidase from Thermotoga maritima'. Together they form a unique fingerprint.

Cite this

Crystal structures of glycoside hydrolase family 51 α-L- arabinofuranosidase from Thermotoga maritima. / Im, Do Hyun; Kimura, Kei Ichi; Hayasaka, Fumitaka; Tanaka, Tomonari; Noguchi, Masato; Kobayashi, Atsushi; Shoda, Shin Ichiro; Miyazaki, Kentaro; Wakagi, Takayoshi; Fushinobu, Shinya.

In: Bioscience, Biotechnology and Biochemistry, Vol. 76, No. 2, 2012, p. 423-428.

Research output: Contribution to journal › Article › peer-review

Im, Do Hyun ; Kimura, Kei Ichi ; Hayasaka, Fumitaka ; Tanaka, Tomonari ; Noguchi, Masato ; Kobayashi, Atsushi ; Shoda, Shin Ichiro ; Miyazaki, Kentaro ; Wakagi, Takayoshi ; Fushinobu, Shinya. / Crystal structures of glycoside hydrolase family 51 α-L- arabinofuranosidase from Thermotoga maritima. In: Bioscience, Biotechnology and Biochemistry. 2012 ; Vol. 76, No. 2. pp. 423-428.

@article{34fdcee7192f4175aac44bc4f1fb4d2b,

title = "Crystal structures of glycoside hydrolase family 51 α-L- arabinofuranosidase from Thermotoga maritima",

abstract = "α-L-Arabinofuranosidase from the hyperthermophilic bacterium Thermotoga maritima (Tm-AFase) is an extremely thermophilic enzyme belonging to glycoside hydrolase family 51. It can catalyze the transglycosylation of a novel glycosyl donor, 4,6-dimethoxy-1,3,5-triazin-2-yl (DMT)-β-D-xylopyranoside. In this study we determined the crystal structures of Tm-AFase in substrate-free and complex forms with arabinose and xylose at 1.8-2.3{\AA} resolution to determine the architecture of the substrate binding pocket. Subsite α1 of Tm-AFase is similar to that of α-L-arabinofuranosidase from Geobacillus stearothermophilus, but the substrate binding pocket of Tm-AFase is narrower and more hydrophobic. Possible substrate binding modes were investigated by automated docking analysis.",

keywords = "Arabinose, Glycoside hydrolase family 51, Thermotoga maritima, Xylose, α-L-arabinofuranosidase",

author = "Im, {Do Hyun} and Kimura, {Kei Ichi} and Fumitaka Hayasaka and Tomonari Tanaka and Masato Noguchi and Atsushi Kobayashi and Shoda, {Shin Ichiro} and Kentaro Miyazaki and Takayoshi Wakagi and Shinya Fushinobu",

note = "Funding Information: We thank the staff of the Photon Factory and SPring-8 for X-ray data collection. Synchrotron beam time at SPring-8 was supported by the Priority Program for Disaster-Affected Quantum Beam Facilities (2011G080 for KEK-PF and 2011A1908 for SPring-8). This study was supported by the New Energy and Industrial Technology Development Organization, and by the International Center of Research and Education for Molecular Complex Chemistry in 2007 of the Tohoku University Global COE Program.",

year = "2012",

doi = "10.1271/bbb.110902",

language = "English",

volume = "76",

pages = "423--428",

journal = "Bioscience, Biotechnology and Biochemistry",

issn = "0916-8451",

publisher = "Japan Society for Bioscience Biotechnology and Agrochemistry",

number = "2",

}

TY - JOUR

T1 - Crystal structures of glycoside hydrolase family 51 α-L- arabinofuranosidase from Thermotoga maritima

AU - Im, Do Hyun

AU - Kimura, Kei Ichi

AU - Hayasaka, Fumitaka

AU - Tanaka, Tomonari

AU - Noguchi, Masato

AU - Kobayashi, Atsushi

AU - Shoda, Shin Ichiro

AU - Miyazaki, Kentaro

AU - Wakagi, Takayoshi

AU - Fushinobu, Shinya

N1 - Funding Information: We thank the staff of the Photon Factory and SPring-8 for X-ray data collection. Synchrotron beam time at SPring-8 was supported by the Priority Program for Disaster-Affected Quantum Beam Facilities (2011G080 for KEK-PF and 2011A1908 for SPring-8). This study was supported by the New Energy and Industrial Technology Development Organization, and by the International Center of Research and Education for Molecular Complex Chemistry in 2007 of the Tohoku University Global COE Program.

PY - 2012

Y1 - 2012

N2 - α-L-Arabinofuranosidase from the hyperthermophilic bacterium Thermotoga maritima (Tm-AFase) is an extremely thermophilic enzyme belonging to glycoside hydrolase family 51. It can catalyze the transglycosylation of a novel glycosyl donor, 4,6-dimethoxy-1,3,5-triazin-2-yl (DMT)-β-D-xylopyranoside. In this study we determined the crystal structures of Tm-AFase in substrate-free and complex forms with arabinose and xylose at 1.8-2.3Å resolution to determine the architecture of the substrate binding pocket. Subsite α1 of Tm-AFase is similar to that of α-L-arabinofuranosidase from Geobacillus stearothermophilus, but the substrate binding pocket of Tm-AFase is narrower and more hydrophobic. Possible substrate binding modes were investigated by automated docking analysis.

AB - α-L-Arabinofuranosidase from the hyperthermophilic bacterium Thermotoga maritima (Tm-AFase) is an extremely thermophilic enzyme belonging to glycoside hydrolase family 51. It can catalyze the transglycosylation of a novel glycosyl donor, 4,6-dimethoxy-1,3,5-triazin-2-yl (DMT)-β-D-xylopyranoside. In this study we determined the crystal structures of Tm-AFase in substrate-free and complex forms with arabinose and xylose at 1.8-2.3Å resolution to determine the architecture of the substrate binding pocket. Subsite α1 of Tm-AFase is similar to that of α-L-arabinofuranosidase from Geobacillus stearothermophilus, but the substrate binding pocket of Tm-AFase is narrower and more hydrophobic. Possible substrate binding modes were investigated by automated docking analysis.

KW - Arabinose

KW - Glycoside hydrolase family 51

KW - Thermotoga maritima

KW - Xylose

KW - α-L-arabinofuranosidase

UR - http://www.scopus.com/inward/record.url?scp=84863242735&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84863242735&partnerID=8YFLogxK

U2 - 10.1271/bbb.110902

DO - 10.1271/bbb.110902

M3 - Article

C2 - 22313787

AN - SCOPUS:84863242735

VL - 76

SP - 423

EP - 428

JO - Bioscience, Biotechnology and Biochemistry

JF - Bioscience, Biotechnology and Biochemistry

SN - 0916-8451

IS - 2

ER -