Three-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site

Most structures of neutral lipases and esterases have been found to adopt t he common alpha/beta hydrolase fold and contain a catalytic Ser-His-Asp tri ad. Some variation occurs in both the overall protein fold and in the locat ion of the catalytic triad, and in some enzymes the role of the aspartate r esidue is replaced by a main-chain carbonyl oxygen atom. Here, we report th e crystal structure of pectin methylesterase that has neither the common al pha/beta hydrolase fold nor the common catalytic triad. The structure of th e Erwinia chrysanthemi enzyme was solved by multiple isomorphous replacemen t and refined at 2.4 Angstrom to a conventional crystallographic X-factor o f 17.9 % (R-free 21.1%). This is the first structure of a pectin methyleste rase and reveals the enzyme to comprise a right-handed parallel beta -helix as seen in the pectinolytic enzymes pectate lyase, pectin lyase, polygalac turonase and rhamnogalacturonase, and unlike the alpha/beta hydrolase fold of rhamnogalacturonan acetylesterase with which it shares esterase activity . Pectin methylesterase has no significant sequence similarity with any pro tein of known structure. Sequence conservation among the pectin methylester ases has been mapped onto the structure and reveals that the active site co mprises two aspartate residues and an arginine residue. These proposed cata lytic residues, located on the solvent-accessible surface of the parallel b eta -helix and in a cleft formed by external loops, are at a location simil ar to that of the active site and substrate-binding cleft of pectate lyase. The structure of pectin methylesterase is an example of a new family of es terases. (C) 2001 Academic Press.