View source for 5gmt


==Crystal structure of the marine PL-14 alginate lyase from Aplysia kurodai==
<StructureSection load='5gmt' size='340' side='right'caption='[[5gmt]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5gmt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aplysia_kurodai Aplysia kurodai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GMT 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]] 1.77&#8491;</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=5gmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmt OCA], [https://pdbe.org/5gmt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gmt RCSB], [https://www.ebi.ac.uk/pdbsum/5gmt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmt ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/E7FLQ2_APLKU E7FLQ2_APLKU] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Alginate is an abundant algal polysaccharide, composed of beta-d-mannuronate and its C5 epimer alpha-l-guluronate, that is a useful biomaterial in cell biology and tissue engineering, with applications in cancer and aging research. The alginate lyase (EC 4.2.2.3) from Aplysia kurodai, AkAly30, is a eukaryotic member of the polysaccharide lyase 14 (PL-14) family and degrades alginate by cleaving the glycosidic bond through a beta-elimination reaction. Here, we present the structural basis for the substrate specificity, with a preference for polymannuronate, of AkAly30. The crystal structure of AkAly30 at a 1.77 A resolution and the putative substrate-binding model show that the enzyme adopts a beta-jelly roll fold at the core of the structure and that Lys-99, Tyr-140, and Tyr-142 form catalytic residues in the active site. Their arrangements allow the carboxyl group of mannuronate residues at subsite +1 to form ionic bonds with Lys-99. The coupled tyrosine forms a hydrogen bond network with the glycosidic bond, and the hydroxy group of Tyr-140 is located near the C5 atom of the mannuronate residue. These interactions could promote the beta-elimination of the mannuronate residue at subsite +1. More interestingly, Gly-118 and the disulfide bond formed by Cys-115 and Cys-124 control the conformation of an active-site loop, which makes the space suitable for substrate entry into subsite -1. The cleavage efficiency of AkAly30 is enhanced relative to that of mutants lacking either Gly-118 or the Cys-115-Cys-124 disulfide bond. The putative binding model and mutagenesis studies provide a novel substrate recognition mode explaining the polymannuronate specificity of PL-14 alginate lyases.

Structure and Polymannuronate Specificity of a Eukaryotic Member of Polysaccharide Lyase Family 14.,Qin HM, Miyakawa T, Inoue A, Nishiyama R, Nakamura A, Asano A, Sawano Y, Ojima T, Tanokura M J Biol Chem. 2017 Feb 10;292(6):2182-2190. doi: 10.1074/jbc.M116.749929. Epub, 2016 Dec 23. PMID:28011642<ref>PMID:28011642</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5gmt" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Aplysia kurodai]]
[[Category: Large Structures]]
[[Category: Miyakawa T]]
[[Category: Nakamura A]]
[[Category: Qin H-M]]
[[Category: Tanokura M]]