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| | <StructureSection load='5j14' size='340' side='right'caption='[[5j14]], [[Resolution|resolution]] 1.92Å' scene=''> | | <StructureSection load='5j14' size='340' side='right'caption='[[5j14]], [[Resolution|resolution]] 1.92Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5j14]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhoh1 Rhoh1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J14 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J14 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5j14]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_hoagii_103S Rhodococcus hoagii 103S]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J14 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J14 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=18C:N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE'>18C</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</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]] 1.915Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5j7z|5j7z]], [[5ccu|5ccu]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=18C:N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE'>18C</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRD_900004:beta-lactose'>PRD_900004</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">REQ_38260 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=685727 RHOH1])</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=5j14 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j14 OCA], [https://pdbe.org/5j14 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j14 RCSB], [https://www.ebi.ac.uk/pdbsum/5j14 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j14 ProSAT]</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=5j14 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j14 OCA], [http://pdbe.org/5j14 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j14 RCSB], [http://www.ebi.ac.uk/pdbsum/5j14 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j14 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Rhoh1]] | + | [[Category: Rhodococcus hoagii 103S]] |
| - | [[Category: Chen, L]] | + | [[Category: Chen L]] |
| - | [[Category: Complex]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
5j14 is a 2 chain structure with sequence from Rhodococcus hoagii 103S. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.915Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
Endoglycoceramidases (EGCases) specifically hydrolyze the glycosidic linkage between the oligosaccharide and the ceramide moieties of various glycosphingolipids, and they have received substantial attention in the emerging field of glycosphingolipidology. However, the mechanism regulating the strict substrate specificity of these GH5 glycosidases has not been identified. In this study, we report a novel EGCase I from Rhodococcus equi 103S (103S_EGCase I) with remarkably broad substrate specificity. Based on phylogenetic analyses, the enzyme may represent a new subfamily of GH5 glycosidases. The X-ray crystal structures of 103S_EGCase I alone and in complex with its substrates monosialodihexosylganglioside (GM3) and monosialotetrahexosylganglioside (GM1) enabled us to identify several structural features that may account for its broad specificity. Compared with EGCase II from Rhodococcus sp. M-777 (M777_EGCase II), which possesses strict substrate specificity, 103S_EGCase I possesses a longer alpha7-helix and a shorter loop 4, which forms a larger substrate-binding pocket that could accommodate more extended oligosaccharides. In addition, loop 2 and loop 8 of the enzyme adopt a more open conformation, which also enlarges the oligosaccharide-binding cavity. Based on this knowledge, a rationally designed experiment was performed to examine the substrate specificity of EGCase II. The truncation of loop 4 in M777_EGCase II increased its activity toward GM1 (163%). Remarkably, the S63G mutant of M777_EGCase II showed a broader substrate spectra and significantly increased activity toward bulky substrates (up to >1370-fold for fucosyl-GM1). Collectively, the results presented here reveal the exquisite substrate recognition mechanism of EGCases and provide an opportunity for further engineering of these enzymes.
Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases.,Han YB, Chen LQ, Li Z, Tan YM, Feng Y, Yang GY J Biol Chem. 2017 Mar 24;292(12):4789-4800. doi: 10.1074/jbc.M116.763821. Epub, 2017 Feb 8. PMID:28179425[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Han YB, Chen LQ, Li Z, Tan YM, Feng Y, Yang GY. Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases. J Biol Chem. 2017 Mar 24;292(12):4789-4800. doi: 10.1074/jbc.M116.763821. Epub, 2017 Feb 8. PMID:28179425 doi:http://dx.doi.org/10.1074/jbc.M116.763821
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