1k5c
From Proteopedia
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Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution
Overview
Crystal structures of endopolygalacturonase from Stereum purpureum were, solved in native and two galacturonic acid complex states at atomic, resolution. Endopolygalacturonase catalyzes the hydrolysis of, alpha-1,4-glycosidic linkage of polygalacturonate in pectin. The native, structure was determined by the multiple wavelength anomalous dispersion, method and was refined anisotropically with SHELXL-97, with an R factor of, 11.4% and an R(free) factor of 14.0% at 0.96 A resolution. The enzyme, folds into a right-handed parallel beta-helix with 10 complete turns. The, crystal structures of its binary complex with one D-galacturonate and its, ternary complex with two D-galacturonates were also determined to identify, the substrate binding site at 1.0 and 1.15 A resolutions, respectively. In, the binary complex, one beta-D-galactopyranuronate was found in the +1, subsite, thus proving the strong affinity of the +1 subsite expected from, the bond cleavage frequency on oligogalacturonates. In the ternary, complex, an additional beta-D-galactofuranuronate was found in the -1, subsite. In both subsites, the recognition of the galacturonate carboxy, group is important in galacturonate binding. In the +1 subsite, the, carboxy group interacts with three basic residues, His195, Arg226, and, Lys228, which were conserved in all endopolygalacturonases. In the -1, subsite, the unique nonprolyl cis-peptide bond is believed to be involved, in binding the carboxy group of the substrate. The active site, architecture of the complexes provides insight into the mechanism of, inverting glycosyl hydrolases and also sheds light on the basis of the, differences between the family 28 and the other inverting glycosyl, hydrolases.
About this Structure
1K5C is a Single protein structure of sequence from Chondrostereum purpureum with NAG, CL and GOL as ligands. Active as Polygalacturonase, with EC number 3.2.1.15 Full crystallographic information is available from OCA.
Reference
Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution., Shimizu T, Nakatsu T, Miyairi K, Okuno T, Kato H, Biochemistry. 2002 May 28;41(21):6651-9. PMID:12022868
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