1VAV

Crystal structure of alginate lyase PA1167 from Pseudomonas aeruginosa at 2.0 A resolution

Summary for 1VAV

• Entry DOI: 10.2210/pdb1vav/pdb
• Descriptor: Alginate lyase PA1167 (2 entities in total)
• Functional Keywords: beta-sandwich, structural genomics, lyase
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 2
• Total formula weight: 50035.69

Authors

Yamasaki, M.,Moriwaki, S.,Miyake, O.,Hashimoto, W.,Murata, K.,Mikami, B. (deposition date: 2004-02-19, release date: 2004-05-25, Last modification date: 2023-12-27)

Primary citation

Yamasaki, M.,Moriwaki, S.,Miyake, O.,Hashimoto, W.,Murata, K.,Mikami, B.
Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.
J.Biol.Chem., 279:31863-31872, 2004

PubMed Abstract: Structural and functional analyses of alginate lyases are important in the clarification of the biofilm-dependent ecosystem in Pseudomonas aeruginosa and in 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 degrees C. 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 A 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 PA1167 of family PL-7 and alpha/alpha-barrel AlgL of family PL-5 may be responsible for the enzyme characteristics. Crystal structures of polysaccharide lyases determined so far indicate that they can be assigned to three 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.

PubMed: 15136569
DOI: 10.1074/jbc.M402466200

Experimental method

X-RAY DIFFRACTION (2 Å)