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| | <StructureSection load='6d2c' size='340' side='right'caption='[[6d2c]], [[Resolution|resolution]] 1.91Å' scene=''> | | <StructureSection load='6d2c' size='340' side='right'caption='[[6d2c]], [[Resolution|resolution]] 1.91Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6d2c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_110082 Cip 110082]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D2C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D2C FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6d2c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nonlabens_ulvanivorans Nonlabens ulvanivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D2C FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.906Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6d3u|6d3u]]</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=6d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d2c OCA], [https://pdbe.org/6d2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d2c RCSB], [https://www.ebi.ac.uk/pdbsum/6d2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d2c ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IL45_01530 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=906888 CIP 110082])</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=6d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d2c OCA], [http://pdbe.org/6d2c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d2c RCSB], [http://www.ebi.ac.uk/pdbsum/6d2c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d2c ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/UL28B_NONUL UL28B_NONUL] Ulvan lyase involved in ulvan degradation (PubMed:29875159). 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 (By similarity).[UniProtKB:G8G2V6]<ref>PMID:29875159</ref> |
| | <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: Cip 110082]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cygler, M]] | + | [[Category: Nonlabens ulvanivorans]] |
| - | [[Category: Ulaganathan, T]] | + | [[Category: Cygler M]] |
| - | [[Category: Lyase]] | + | [[Category: Ulaganathan T]] |
| - | [[Category: Structure of nlr48]]
| + | |
| Structural highlights
Function
UL28B_NONUL Ulvan lyase involved in ulvan degradation (PubMed:29875159). 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 (By similarity).[UniProtKB:G8G2V6][1]
Publication Abstract from PubMed
Ulvan is a complex sulfated polysaccharide present in the cell wall of green algae of the genus Ulva (Chlorophyta). The first ulvan-degrading polysaccharide lyases were identified several years ago, and more were discovered through genome sequencing of marine bacteria. Ulvan lyases are now grouped in three polysaccharide lyase (PL) families in the CAZy database, PL24, PL25, and PL28. The recently determined structures of the representative lyases from families PL24 and PL25 show that they adopt a seven-bladed beta-propeller fold and utilize the His/Tyr catalytic mechanism. No structural information is yet available for PL28 ulvan lyases. NLR48 from Nonlabens ulvanivorans belongs to PL28 together with its close paralog, NLR42. Biochemical studies of NLR42 have revealed that it can cleave ulvan next to both uronic acid epimers. We report the crystal structure of ulvan lyase NLR48 at 1.9-A resolution. It has a beta-jelly roll fold with an extended, deep, and positively charged substrate-binding cleft. Putative active-site residues were identified from the sequence conservation pattern, and their role was confirmed by site-directed mutagenesis. The structure of an inactive K162M mutant with a tetrasaccharide substrate showed the substrate occupying the "-" subsites. Comparison with lyases from other PL families with beta-jelly roll folds supported assignment of the active site and explained its ability to degrade ulvan next to either epimer of uronic acid. NLR48 contains the His/Tyr catalytic machinery with Lys(162) and Tyr(281) playing the catalytic base/acid roles.
Structural and functional characterization of PL28 family ulvan lyase NLR48 from Nonlabens ulvanivorans.,Ulaganathan T, Banin E, Helbert W, Cygler M J Biol Chem. 2018 Jul 20;293(29):11564-11573. doi: 10.1074/jbc.RA118.003659. Epub, 2018 Jun 6. PMID:29875159[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ulaganathan T, Banin E, Helbert W, Cygler M. Structural and functional characterization of PL28 family ulvan lyase NLR48 from Nonlabens ulvanivorans. J Biol Chem. 2018 Jul 20;293(29):11564-11573. doi: 10.1074/jbc.RA118.003659. Epub, 2018 Jun 6. PMID:29875159 doi:http://dx.doi.org/10.1074/jbc.RA118.003659
- ↑ Ulaganathan T, Banin E, Helbert W, Cygler M. Structural and functional characterization of PL28 family ulvan lyase NLR48 from Nonlabens ulvanivorans. J Biol Chem. 2018 Jul 20;293(29):11564-11573. doi: 10.1074/jbc.RA118.003659. Epub, 2018 Jun 6. PMID:29875159 doi:http://dx.doi.org/10.1074/jbc.RA118.003659
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