7o84

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Current revision (07:50, 1 May 2024) (edit) (undo)
 
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<StructureSection load='7o84' size='340' side='right'caption='[[7o84]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
<StructureSection load='7o84' size='340' side='right'caption='[[7o84]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[7o84]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Psesl Psesl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O84 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[7o84]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudopedobacter_saltans_DSM_12145 Pseudopedobacter saltans DSM 12145]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O84 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAW:4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC+ACID'>MAW</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.177&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7o7a|7o7a]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAW:4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC+ACID'>MAW</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pedsa_0632 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=762903 PSESL])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7o84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o84 OCA], [https://pdbe.org/7o84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o84 RCSB], [https://www.ebi.ac.uk/pdbsum/7o84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o84 ProSAT]</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=7o84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o84 OCA], [https://pdbe.org/7o84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o84 RCSB], [https://www.ebi.ac.uk/pdbsum/7o84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o84 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/F0S7Y7_PSESL F0S7Y7_PSESL]
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The Polysaccharide Lyase Family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1-3. To decipher the mode of recognition and action of the enzymes belonging to subfamily PL6_1, we solved the crystal structures of Pedsa0632, Patl3640, Pedsa3628 and Pedsa3807, which all show different substrate specificities and mode of action (endo-/exo-lyase). Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirm that the conserved residues in subsites -1 to +3 of the catalytic site form a common platform which can accommodate various types of alginate in a very similar manner but with a series of original adaptations bringing them their specificities of action. From comparative studies with existing structures of PL6_1 alginate lyases, we observe that in the right-handed parallel beta-helix fold shared by all these enzymes, the substrate binding site harbors the same overall conserved structures and organization. Despite this apparent similarity, it appears that members of the PL6_1 subfamily specifically accommodate and catalyze the degradation of different alginates suggesting that this common platform is actually a highly adaptable and specific tool.
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Exploring molecular determinants of polysaccharide Lyase family 6-1 enzyme activity.,Violot S, Galisson F, Carrique L, Jugnarain V, Conchou L, Robert X, Thureau A, Helbert W, Aghajari N, Ballut L Glycobiology. 2021 Jul 10. pii: 6318796. doi: 10.1093/glycob/cwab073. PMID:34245266<ref>PMID:34245266</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 7o84" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Psesl]]
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[[Category: Pseudopedobacter saltans DSM 12145]]
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[[Category: Aghajari, N]]
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[[Category: Aghajari N]]
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[[Category: Ballut, L]]
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[[Category: Ballut L]]
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[[Category: Carrique, L]]
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[[Category: Carrique L]]
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[[Category: Violot, S]]
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[[Category: Violot S]]
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[[Category: Beta helix]]
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[[Category: Lyase]]
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Current revision

Structure of the PL6 family alginate lyase Pedsa0632 from Pseudopedobacter saltans in complex with substrate

PDB ID 7o84

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