6byt

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Complex structure of LOR107 mutant (R320) with tetrasaccharide substrate

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Categories: Alteromonas sp. LOR | Large Structures | Cygler M | Ulaganathan TS

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 <StructureSection load='6byt' size='340' side='right'caption='[[6byt]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6byt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alteromonas_sp._lor Alteromonas sp. lor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BYT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6byt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Alteromonas_sp._LOR Alteromonas sp. LOR]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BYT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=83Y:6-DEOXY-3-O-SULFO-ALPHA-L-MANNOPYRANOSE'>83Y</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GCB:D-SACCHARIC+ACID+1,5-LACTONE'>GCB</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LOR_107 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1537994 Alteromonas sp. LOR])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=83Y:6-DEOXY-3-O-SULFO-ALPHA-L-MANNOPYRANOSE'>83Y</scene>, <scene name='pdbligand=BDP:BETA-D-GLUCOPYRANURONIC+ACID'>BDP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6byt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byt OCA], [http://pdbe.org/6byt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6byt RCSB], [http://www.ebi.ac.uk/pdbsum/6byt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6byt 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=6byt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byt OCA], [https://pdbe.org/6byt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6byt RCSB], [https://www.ebi.ac.uk/pdbsum/6byt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6byt ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/UL24S_ALTSL UL24S_ALTSL] Ulvan lyase involved in ulvan degradation. Ulvan is the main polysaccharide component of the Ulvales (green seaweed) cell wall. It is composed of disaccharide building blocks comprising 3-sulfated rhamnose (Rha3S) linked to D-glucuronic acid (GlcA), L-iduronic acid (IduA), or D-xylose (Xyl). Ulvan lyase catalyzes preferentially the endolytic cleavage of the glycosidic bond between Rha3S and the uronic acid GlcA, but not IduA, producing oligosaccharides that have unsaturated 4-deoxy-L-threo-hex-4-enopyranosiduronic acid (deltaUA) at the non-reducing end. The most abundant end products in the degradation of the ulvan polysaccharide were deltaUA-Rha3S disaccharides and deltaUA-Rha3S-IduA-Rha3S and deltaUA-Rha3S-Xyl-Rha3S tetrasaccharides.<ref>PMID:26763234</ref>
-Ulvan is a major cell wall component of green algae of the genus Ulva and some marine bacteria encode enzymes that can degrade this polysaccharide. The first ulvan degrading lyases have been recently characterized and several putative ulvan lyases have been recombinantly expressed, confirmed as ulvan lyases and partially characterized. Two families of ulvan degrading lyases, PL24 and PL25, have recently been established. The PL24 lyase LOR_107 from the bacterial Alteromonadales sp. strain LOR degrades ulvan endolytically, cleaving the bond at the C4 of a glucuronic acid. However, the mechanism and LOR_107 structural features involved are unknown. We present here the crystal structure of LOR_107, representing the first PL24 family structure. We found that LOR_107 adopts a seven-bladed beta-propeller fold with a deep canyon on one side of the protein. Comparative sequence analysis revealed a cluster of conserved residues within this canyon, and site-directed mutagenesis disclosed several residues essential for catalysis. We also found that LOR_107 uses the His/Tyr catalytic mechanism, common to several PL families. We captured a tetrasaccharide substrate in the structures of two inactive mutants, which indicated a two-step binding event, with the first substrate interaction near the top of the canyon coordinated by Arg-320, followed by sliding of the substrate into the canyon toward the active-site residues. Surprisingly, the LOR_107 structure was very similar to that of PL25 family PLSV_3936, despite only ~14% sequence identity between the two enzymes. On the basis of our structural and mutational analyses, we propose a catalytic mechanism for LOR_107 that differs from the typical His/Tyr mechanism.
-Structure-function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism.,Ulaganathan T, Helbert W, Kopel M, Banin E, Cygler M J Biol Chem. 2018 Jan 30. pii: RA117.001642. doi: 10.1074/jbc.RA117.001642. PMID:29382716<ref>PMID:29382716</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6byt" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Alteromonas sp. lor]]
+[[Category: Alteromonas sp. LOR]]
 [[Category: Large Structures]]
-[[Category: Cygler, M]]
+[[Category: Cygler M]]
-[[Category: Ulaganathan, T S]]
+[[Category: Ulaganathan TS]]
-[[Category: Lyase]]

6byt

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Complex structure of LOR107 mutant (R320) with tetrasaccharide substrate

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