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Published online before print July 5, 2006, 10.1110/ps.062220206
Protein Science (2006), 15:1951-1960. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: Structural insights into alkalophilicity and implications for adaptation to polyextreme conditions

Karuppasamy Manikandan1, Amit Bhardwaj2, Naveen Gupta3, Neratur K. Lokanath4, Amit Ghosh3, Vanga Siva Reddy2 and Suryanarayanarao Ramakumar1,5

1 Department of Physics, Indian Institute of Science, Bangalore 560 012, India
2 International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
3 Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India
4 Advanced Protein Crystallography Research Group, RIKEN Harima Institute, Hyogo 6795148, Japan
5 Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India

(RECEIVED March 15, 2006; FINAL REVISION May 15, 2006; ACCEPTED May 15, 2006)

Crystal structures are known for several glycosyl hydrolase family 10 (GH10) xylanases. However, none of them is from an alkalophilic organism that can grow in alkaline conditions. We have determined the crystal structures at 2.2 Å of a GH10 extracellular endoxylanase (BSX) from an alkalophilic Bacillus sp. NG-27, for the native and the complex enzyme with xylosaccharides. The industrially important enzyme is optimally active and stable at 343 K and at a pH of 8.4. Comparison of the structure of BSX with those of other thermostable GH10 xylanases optimally active at acidic or close to neutral pH showed that the solvent-exposed acidic amino acids, Asp and Glu, are markedly enhanced in BSX, while solvent-exposed Asn was noticeably depleted. The BSX crystal structure when compared with putative three-dimensional homology models of other extracellular alkalophilic GH10 xylanases from alkalophilic organisms suggests that a protein surface rich in acidic residues may be an important feature common to these alkali thermostable enzymes. A comparison of the surface features of BSX and of halophilic proteins allowed us to predict the activity of BSX at high salt concentrations, which we verified through experiments. This offered us important lessons in the polyextremophilicity of proteins, where understanding the structural features of a protein stable in one set of extreme conditions provided clues about the activity of the protein in other extreme conditions. The work brings to the fore the role of the nature and composition of solvent-exposed residues in the adaptation of enzymes to polyextreme conditions, as in BSX.

Keywords: alkali thermostable; GH10 xylanase; solvent-exposed acidic residues; solvent-exposed basic residues; polyextremophilicity; alkalophilic organism


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