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| | ==Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution== | | ==Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution== |
| - | <StructureSection load='1k5c' size='340' side='right' caption='[[1k5c]], [[Resolution|resolution]] 0.96Å' scene=''> | + | <StructureSection load='1k5c' size='340' side='right'caption='[[1k5c]], [[Resolution|resolution]] 0.96Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K5C FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1k5c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chondrostereum_purpureum Chondrostereum purpureum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K5C FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.96Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kcc|1kcc]], [[1kcd|1kcd]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [https://pdbe.org/1k5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [https://www.ebi.ac.uk/pdbsum/1k5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k5c ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5c OCA], [http://pdbe.org/1k5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k5c RCSB], [http://www.ebi.ac.uk/pdbsum/1k5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k5c ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/P79074_9AGAR P79074_9AGAR] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/1k5c_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/1k5c_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Chondrostereum purpureum]] | | [[Category: Chondrostereum purpureum]] |
| - | [[Category: Polygalacturonase]] | + | [[Category: Large Structures]] |
| - | [[Category: Kato, H]] | + | [[Category: Kato H]] |
| - | [[Category: Miyairi, K]] | + | [[Category: Miyairi K]] |
| - | [[Category: Nakatsu, T]] | + | [[Category: Nakatsu T]] |
| - | [[Category: Okuno, T]] | + | [[Category: Okuno T]] |
| - | [[Category: Shimizu, T]] | + | [[Category: Shimizu T]] |
| - | [[Category: Beta helical structure]]
| + | |
| - | [[Category: Glycoside hydrolase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Silver-leaf inducing substance]]
| + | |
| Structural highlights
Function
P79074_9AGAR
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shimizu T, Nakatsu T, Miyairi K, Okuno T, Kato H. Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution. Biochemistry. 2002 May 28;41(21):6651-9. PMID:12022868
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