5uam

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Current revision (14:25, 6 March 2024) (edit) (undo)
 
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<StructureSection load='5uam' size='340' side='right'caption='[[5uam]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
<StructureSection load='5uam' size='340' side='right'caption='[[5uam]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5uam]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UAM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UAM FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5uam]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoalteromonas_sp._PLSV Pseudoalteromonas sp. PLSV]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UAM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UAM 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.45&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5uam FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uam OCA], [http://pdbe.org/5uam PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uam RCSB], [http://www.ebi.ac.uk/pdbsum/5uam PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uam ProSAT]</span></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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5uam FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uam OCA], [https://pdbe.org/5uam PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uam RCSB], [https://www.ebi.ac.uk/pdbsum/5uam PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uam 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/UL25_PSEXP UL25_PSEXP] 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 the endolytic cleavage of the glycosidic bond between Rha3S and the uronic acids GlcA or IduA, producing oligosaccharides that have unsaturated 4-deoxy-L-threo-hex-4-enopyranosiduronic acid (deltaUA) at the non-reducing end. This results eventually in the degradation of the ulvan polysaccharide into deltaUA-Rha3S disaccharides and deltaUA-Rha3S-Xyl-Rha3S tetrasaccharides.<ref>PMID:28290654</ref>
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Ulvan is a complex sulfated polysaccharide biosynthesized by green seaweed and contains predominantly rhamnose, xylose, and uronic acid sugars. Ulvan-degrading enzymes have only recently been identified and added to the CAZy ( www.cazy.org ) database as family PL24, but neither their structure nor catalytic mechanism(s) are yet known. Several homologous, new ulvan lyases, have been discovered in Pseudoalteromonas sp. strain PLSV, Alteromonas LOR, and Nonlabens ulvanivorans, defining a new family PL25, with the lyase encoded by the gene PLSV_3936 being one of them. This enzyme cleaves the glycosidic bond between 3-sulfated rhamnose (R3S) and glucuronic acid (GlcA) or iduronic acid (IdoA) via a beta-elimination mechanism. We report the crystal structure of PLSV_3936 and its complex with a tetrasaccharide substrate. PLSV_3936 folds into a seven-bladed beta-propeller, with each blade consisting of four antiparallel beta-strands. Sequence conservation analysis identified a highly conserved region lining at one end of a deep crevice on the protein surface. The putative active site was identified by mutagenesis and activity measurements. Crystal structure of the enzyme with a bound tetrasaccharide substrate confirmed the identity of base and acid residues and allowed determination of the catalytic mechanism and also the identification of residues neutralizing the uronic acid carboxylic group. The PLSV_3936 structure provides an example of a convergent evolution among polysaccharide lyases toward a common active site architecture embedded in distinct folds.
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New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture.,Ulaganathan T, Boniecki MT, Foran E, Buravenkov V, Mizrachi N, Banin E, Helbert W, Cygler M ACS Chem Biol. 2017 Mar 23. doi: 10.1021/acschembio.7b00126. PMID:28290654<ref>PMID:28290654</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 5uam" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Boniecki, M T]]
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[[Category: Pseudoalteromonas sp. PLSV]]
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[[Category: Cygler, M]]
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[[Category: Boniecki MT]]
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[[Category: Ulaganathan, T S]]
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[[Category: Cygler M]]
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[[Category: Beta propellar fold]]
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[[Category: Ulaganathan TS]]
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[[Category: Degrades ulvan polysaccharide]]
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[[Category: Lyase]]
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Current revision

Structure of a new family of Polysaccharide lyase PL25-Ulvanlyase.

PDB ID 5uam

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