Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.
Enzyme-catalyzed beta-elimination of sugar uronic acids, exemplified by the degradation of plant cell wall pectins, plays an important role in a wide spectrum of biological processes ranging from the recycling of plant biomass through to pathogen virulence. The three-dimensional crystal structure of the catalytic module of a "family PL-10" polysaccharide lyase, Pel10Acm from Cellvibrio japonicus, solved at a resolution of 1.3 A, reveals a new polysaccharide lyase fold and is the first example of a polygalacturonic acid lyase that does not exhibit the "parallel beta-helix" topology. The "Michaelis" complex of an inactive mutant in association with the substrate trigalacturonate/Ca2+ reveals the catalytic machinery harnessed by this polygalacturonate lyase, which displays a stunning resemblance, presumably through convergent evolution, to the tetragalacturonic acid complex observed for a structurally unrelated polygalacturonate lyase from family PL-1. Common coordination of the -1 and +1 subsite saccharide carboxylate groups by a protein-liganded Ca2+ ion, the positioning of an arginine catalytic base in close proximity to the alpha-carbon hydrogen and numerous other conserved enzyme-substrate interactions, considered in light of mutagenesis data for both families, suggest a generic polysaccharide anti-beta-elimination mechanism.
Charnock
Simon J
SJ
York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom.
Brown
Ian E
IE
Turkenburg
Johan P
JP
Black
Gary W
GW
Davies
Gideon J
GJ
D020134:Catalytic Domain / Q000235:genetics; D020633:Cellvibrio / Q000201:enzymology / Q000235:genetics; D018360:Crystallography, X-Ray; D019143:Evolution, Molecular; D007700:Kinetics; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D011133:Polysaccharide-Lyases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D055672:Static Electricity; D013379:Substrate Specificity; D013400:Sugar Acids / Q000737:chemistry / Q000378:metabolism; D014312:Trisaccharides / Q000737:chemistry / Q000378:metabolism
D011994:Recombinant Proteins; D013400:Sugar Acids; D014312:Trisaccharides; C065008:O-galactopyranosyluronic acid-(1-4)-O-galactopyranosyluronic acid-(1-4)-galactopyranosyluronic acid; D011133:Polysaccharide-Lyases