Determination of Three-Dimensional Structure of Xylan-Binding Xylanase from Bacillus firmus K-1 by Homology Modeling

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Pattraporn Jommuengbout
King Mongkut's University of Technology Thonburi, Bangmod, Toongkru, Bangkok 10140
Khin Lay Kyu
King Mongkut's University of Technology Thonburi, Bangmod, Toongkru, Bangkok 10140
Khanok Ratanakhanokchai
King Mongkut's University of Technology Thonburi, Bangmod, Toongkru, Bangkok 10140
Surapong Pinitglang
University of the Thai Chamber of Commerce, Dindaeng, Bangkok 10400

Abstract

Three-dimensional structure of xylan-binding xylanase (XBX) from Bacillus firmus K-1 whichhad been cloned and expressed xbx in Escherichia coli was determined by homology modeling usingthe X-ray structure of Bacillus circulans (1BVV) xylanase as a template. The result showed that thethree-dimensional structure of XBX had a shape as a çclosed right handé. It contains 14 β-sheets and1 α-helix. The catalytic sites of XBX are Glu78 and Glu171, which are located opposite to each otherin an open cleft and reach into this cleft. Glu78, which is nucleophile, holds in place by interaction toGln126, Tyr69 and Tyr80, while Glu171, which is acid/base catalyst, forms hydrogen bond with onlyAsn35. The same Root mean square deviation (RMSD) which was obtained from superpositionbackbone structure and each atom between XBX and 1BVV were 0.329 Å. These results revealthree-dimensional structure from homology modeling is correctable and believable. This method is analternative for determination of the three-dimensional structure of enzyme within a short time.

Keywords : Bacillus firmus K-1 / Homology Modeling / Three-dimensional Structure /Xylan-Binding Xylanase

Article Details

Issue
Vol. 29 No. 3 (2006): July - September
Section
Original Articles
Author Biographies

Pattraporn Jommuengbout, King Mongkut's University of Technology Thonburi, Bangmod, Toongkru, Bangkok 10140

Graduate Student, Division of Biochemical Technology, School of Bioresources and Technology.

Khin Lay Kyu, King Mongkut's University of Technology Thonburi, Bangmod, Toongkru, Bangkok 10140

Assistant Professor, Division of Biochemical Technology, School of Bioresources and Technology.

Khanok Ratanakhanokchai, King Mongkut's University of Technology Thonburi, Bangmod, Toongkru, Bangkok 10140

Assistant Professor, Division of Biochemical Technology, School of Bioresources and Technology.

Surapong Pinitglang, University of the Thai Chamber of Commerce, Dindaeng, Bangkok 10400

Assistant Professor, Department of Food Science and Technology, Facutty of Science.