6kzk
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
==Structure of alginate lyase Aly36B mutant K143A/M171A in complex with alginate trisaccharide== | ==Structure of alginate lyase Aly36B mutant K143A/M171A in complex with alginate trisaccharide== | ||
| - | <StructureSection load='6kzk' size='340' side='right'caption='[[6kzk]]' scene=''> | + | <StructureSection load='6kzk' size='340' side='right'caption='[[6kzk]], [[Resolution|resolution]] 2.79Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KZK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KZK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6kzk]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Chitinophaga_sp._md30 Chitinophaga sp. md30]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KZK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KZK FirstGlance]. <br> |
| - | </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=6kzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kzk OCA], [http://pdbe.org/6kzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kzk RCSB], [http://www.ebi.ac.uk/pdbsum/6kzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kzk ProSAT]</span></td></tr> | + | </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=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene></td></tr> |
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CK934_20815 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2033437 Chitinophaga sp. MD30])</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=6kzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kzk OCA], [http://pdbe.org/6kzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kzk RCSB], [http://www.ebi.ac.uk/pdbsum/6kzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kzk ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Alginate lyases, which are important in both basic and applied sciences, fall into ten polysaccharide lyase (PL) families. PL36 is a newly established family that includes 39 bacterial sequences and one eukaryotic sequence. Till now, the structures or catalytic mechanisms of PL36 alginate lyases have yet to be revealed. Here, we characterized a novel PL36 alginate lyase, Aly36B, from Chitinophaga sp. MD30. Aly36B is a polymannuronate specific endolytic alginate lyase. To probe the catalytic mechanism of Aly36B, the structures of wild-type Aly36B and its mutants (K143A/Y185A in complex with alginate tetrasaccharide and K143A/M171A with trisaccharide) were solved. The overall structure of Aly36B belongs to the beta-jelly roll scaffold, adopting a typical beta-sandwich fold. Aly36B contains a Ca(2+), which is far away from the active center and plays an important role in stabilizing the structure of Aly36B. Based on structural and mutational analyses, the catalytic mechanism of Aly36B for alginate degradation was explained. During catalysis, Arg(169), Tyr(185), and Tyr(187) are responsible for neutralizing the negative charge of the substrate, and Lys(143) acts as both the catalytic base and the catalytic acid, which represents a new kind of catalytic mechanism of alginate lyases. Sequence alignment shows that these four residues involved in catalysis are highly conserved in all PL36 sequences, suggesting that PL36 alginate lyases may adopt a similar catalytic mechanism. Taken together, this study reveals the molecular structure and catalytic mechanism of a PL36 alginate lyase, broadening our knowledge on alginate lyases and facilitating future biotechnological applications of PL36 alginate lyases. | ||
| + | |||
| + | Alginate Lyase Aly36B is a New Bacterial Member of the Polysaccharide Lyase Family 36 and Catalyzes by a Novel Mechanism With Lysine as Both the Catalytic Base and Catalytic Acid.,Dong F, Xu F, Chen XL, Li PY, Li CY, Li FC, Chen Y, Wang P, Zhang YZ J Mol Biol. 2019 Dec 6;431(24):4897-4909. doi: 10.1016/j.jmb.2019.10.023. Epub, 2019 Nov 1. PMID:31682837<ref>PMID:31682837</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6kzk" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Chitinophaga sp. md30]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Chen | + | [[Category: Chen, X L]] |
| - | [[Category: Dong F]] | + | [[Category: Dong, F]] |
| - | [[Category: Zhang | + | [[Category: Zhang, Y Z]] |
| + | [[Category: Lyase]] | ||
Revision as of 05:58, 20 January 2021
Structure of alginate lyase Aly36B mutant K143A/M171A in complex with alginate trisaccharide
| |||||||||||
