1k5c
From Proteopedia
(New page: 200px<br /><applet load="1k5c" size="450" color="white" frame="true" align="right" spinBox="true" caption="1k5c, resolution 0.96Å" /> '''Endopolygalacturonas...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1k5c.jpg|left|200px]]<br /><applet load="1k5c" size=" | + | [[Image:1k5c.jpg|left|200px]]<br /><applet load="1k5c" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1k5c, resolution 0.96Å" /> | caption="1k5c, resolution 0.96Å" /> | ||
'''Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution'''<br /> | '''Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Crystal structures of endopolygalacturonase from Stereum purpureum were | + | 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== | ==About this Structure== | ||
| - | 1K5C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum] with NAG, CL and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] Full crystallographic information is available from [http:// | + | 1K5C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum] with <scene name='pdbligand=NAG:'>NAG</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. |
==Reference== | ==Reference== | ||
| Line 26: | Line 26: | ||
[[Category: silver-leaf inducing substance]] | [[Category: silver-leaf inducing substance]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:30:20 2008'' |
Revision as of 11:30, 21 February 2008
|
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 , and 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
Page seeded by OCA on Thu Feb 21 13:30:20 2008
