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| | <StructureSection load='7byx' size='340' side='right'caption='[[7byx]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='7byx' size='340' side='right'caption='[[7byx]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7byx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chrysosporium_pruinosum_(gilman_&_abbott)_carmich. Chrysosporium pruinosum (gilman & abbott) carmich.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BYX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BYX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7byx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Phanerodontia_chrysosporium Phanerodontia chrysosporium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BYX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7bys|7bys]], [[7byt|7byt]], [[7byv|7byv]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pc1,3Gal43A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5306 Chrysosporium pruinosum (Gilman & Abbott) Carmich.])</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=7byx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byx OCA], [https://pdbe.org/7byx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7byx RCSB], [https://www.ebi.ac.uk/pdbsum/7byx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7byx ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Galactan_1,3-beta-galactosidase Galactan 1,3-beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.145 3.2.1.145] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7byx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byx OCA], [http://pdbe.org/7byx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7byx RCSB], [http://www.ebi.ac.uk/pdbsum/7byx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7byx ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q50KB2_PHACH Q50KB2_PHACH] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Galactan 1,3-beta-galactosidase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Fujimoto, Z]] | + | [[Category: Phanerodontia chrysosporium]] |
| - | [[Category: Igarashi, K]] | + | [[Category: Fujimoto Z]] |
| - | [[Category: Ishida, T]] | + | [[Category: Igarashi K]] |
| - | [[Category: Kaneko, S]] | + | [[Category: Ishida T]] |
| - | [[Category: Kishine, N]] | + | [[Category: Kaneko S]] |
| - | [[Category: Matsuyama, K]] | + | [[Category: Kishine N]] |
| - | [[Category: 3-galactanase]]
| + | [[Category: Matsuyama K]] |
| - | [[Category: 3-galactotriose]]
| + | |
| - | [[Category: Arabinogalactan degrade]]
| + | |
| - | [[Category: Carbohydrate binding module family 35]]
| + | |
| - | [[Category: Complex with beta-1]]
| + | |
| - | [[Category: Exo-beta-1]]
| + | |
| - | [[Category: Glycoside hydrolase family 43]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
7byx is a 4 chain structure with sequence from Phanerodontia chrysosporium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.3Å |
| Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q50KB2_PHACH
Publication Abstract from PubMed
Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-beta-1,3-galactanase is a glycoside hydrolase from the basidiomycete Phanerochaete chrysosporium (Pc1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of Pc1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family (CBM) 35 binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveal that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. Pc1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the beta-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly->Trp substitution, which affects pyranose stacking, and an Asp->Asn substitution in the binding pocket, which recognizes beta-linked rather than alpha-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.
Unique active site and subsite features in the arabinogalactan-degrading GH43 exo-beta-1,3-galactanase from Phanerochaete chrysosporium.,Matsuyama K, Kishine N, Fujimoto Z, Sunagawa N, Kotake T, Tsumuraya Y, Samejima M, Igarashi K, Kaneko S J Biol Chem. 2020 Oct 22. pii: RA120.016149. doi: 10.1074/jbc.RA120.016149. PMID:33093171[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Matsuyama K, Kishine N, Fujimoto Z, Sunagawa N, Kotake T, Tsumuraya Y, Samejima M, Igarashi K, Kaneko S. Unique active site and subsite features in the arabinogalactan-degrading GH43 exo-beta-1,3-galactanase from Phanerochaete chrysosporium. J Biol Chem. 2020 Oct 22. pii: RA120.016149. doi: 10.1074/jbc.RA120.016149. PMID:33093171 doi:http://dx.doi.org/10.1074/jbc.RA120.016149
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