View source for 5gkq


==Structure of PL6 family alginate lyase AlyGC mutant-R241A==
<StructureSection load='5gkq' size='340' side='right'caption='[[5gkq]], [[Resolution|resolution]] 2.56&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5gkq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraglaciecola_chathamensis_S18K6 Paraglaciecola chathamensis S18K6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GKQ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.565&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=5gkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkq OCA], [https://pdbe.org/5gkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gkq RCSB], [https://www.ebi.ac.uk/pdbsum/5gkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkq ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0A1S4NYD8_9ALTE A0A1S4NYD8_9ALTE] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Alginate lyases that degrade alginate via a beta-elimination reaction fall into seven polysaccharide lyase (PL) families. Although the structures and catalytic mechanisms of alginate lyases in the other PL families have been clarified, those in family PL6 have yet to be revealed. Here, the crystal structure of AlyGC, a PL6 alginate lyase from marine bacterium Glaciecola chathamensis S18K6T, was solved, and its catalytic mechanism was illustrated. AlyGC is a homodimeric enzyme and adopts a structure distinct from other alginate lyases. Each monomer contains a catalytic N-terminal domain and a functionally unknown C-terminal domain. A combined structural and mutational analysis using the structures of AlyGC and of an inactive mutant R241A in complex with an alginate tetrasaccharide indicates that conformational changes occur in AlyGC when a substrate is bound and that the two active centers in AlyGC may not bind substrates simultaneously. The C-terminal domain is shown to be essential for the dimerization and the catalytic activity of AlyGC. Residues Tyr130, Arg187, His242, Arg265, and Tyr304 in the active center are also important for the activity of AlyGC. In catalysis, Lys220 and Arg241 function as the Bronsted base and acid, respectively, and a Ca2+ in the active center neutralizes the negative charge of the C5 carboxyl group of the substrate. Finally, based on our data, we propose a metal ion-assisted catalytic mechanism of AlyGC for alginate cleavage with a state change mode, which provides a better understanding for polysaccharide lyases and alginate degradation.

Novel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6.,Xu F, Dong F, Wang P, Cao HY, Li CY, Li PY, Pang XH, Zhang YZ, Chen XL J Biol Chem. 2017 Mar 17;292(11):4457-4468. doi: 10.1074/jbc.M116.766030. Epub, 2017 Feb 1. PMID:28154171<ref>PMID:28154171</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5gkq" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Paraglaciecola chathamensis S18K6]]
[[Category: Wang P]]
[[Category: Xu F]]
[[Category: Zhang YZ]]