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Papers In Press, published online ahead of print May 10, 2004
J. Biol. Chem, 10.1074/jbc.M402466200
Submitted on March 4, 2004
Revised on April 28, 2004
Accepted on May 10, 2004

Structure and function of a hypothetical pseudomonas aeruginosa protein PA1167 classified into family PL-7: A novel alginate lyase with a beta-sandwich fold

Masayuki Yamasaki, Satoko Moriwaki, Osamu Miyake, Wataru Hashimoto, Kousaku Murata, and Bunzo Mikami

Department of Basic and Applied Molecular Biotechnology, Division of Food and Biological Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011

Corresponding Author: murata{at}food2.food.kyoto-u.ac.jp

Structural and functional analyses of alginate lyases are important in the clarification of the biofilm-dependent ecosystem in P. aeruginosa, and the development of therapeutic agents for bacterial disease. Most alginate lyases are classified into polysaccharide lyase (PL) family-5 and -7 based on their primary structures. Family PL-7 enzymes are still poorly characterized especially in structural properties. Among family PL-7, a gene coding for a hypothetical protein (PA1167) homologous to Sphingomonas alginate lyase A1-II was found to be present in the P. aeruginosa genome. PA1167 overexpressed in Escherichia coli cleaved glycosidic bonds in alginate and released unsaturated saccharides, indicating that PA1167 is an alginate lyase catalyzing a beta -elimination reaction. The enzyme acted preferably on heteropolymeric regions endolytically, and worked most efficiently at pH 8.5 and 40. The specific activity of PA1167, however, was much weaker than that of the known alginate lyase AlgL, suggesting that AlgL plays a main role in alginate depolymerization in P. aeruginosa. In addition to this specific activity, differences were found between PA1167 and AlgL in enzyme properties such as molecular mass, optimum pH, salt effect, and substrate specificity. The first crystal structure of the family PL-7 alginate lyase was determined at 2.0 resolution. PA1167 was found to form a glove-like beta -sandwich composed of 15 beta -strands and 3 alpha -helices. The structural difference between the beta -sandwich PA1167of family PL-7 and alpha /alpha -barrel AlgL of family PL-5 may be responsible for the enzyme characteristics. Crystal structures of polysaccharide lyases so far determined indicate that they can be assigned to 3 folding groups having parallel beta -helix, alpha /alpha -barrel, and alpha /alpha -barrel + antiparallel beta -sheet structures as basic frames. PA1167 is the fourth novel folding structure found among polysaccharide lyases.


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