View source for 6kfn


==Crystal structure of alginate lyase from Paenibacillus sp. str. FPU-7==
<StructureSection load='6kfn' size='340' side='right'caption='[[6kfn]], [[Resolution|resolution]] 0.89&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6kfn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_sp._FPU-7 Paenibacillus sp. FPU-7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KFN 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]] 0.89&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6kfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kfn OCA], [https://pdbe.org/6kfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kfn RCSB], [https://www.ebi.ac.uk/pdbsum/6kfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kfn ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A novel alginate lyase, PsAly, with a molecular mass of 33 kDa and whose amino acid sequence shares no significant similarity to other known proteins, was biochemically and structurally characterised from Paenibacillus sp. str. FPU-7. The maximum PsAly activity was obtained at 65 degrees C, with an optimum pH of pH 7-7.5. The activity was enhanced by divalent cations, such as Mg(2+), Mn(2+), or Co(2+), and inhibited by a metal chelator, ethylenediaminetetraacetic acid. The reaction products indicated that PsAly is an endolytic enzyme with a preference for polymannuronate. Herein, we report a detailed crystal structure of PsAly at a resolution of 0.89 A, which possesses a beta-helix fold that creates a long cleft. The catalytic site was different from that of other polysaccharide lyases. Site-directed mutational analysis of conserved residues predicted Tyr184 and Lys221 as catalytic residues, abstracting from the C5 proton and providing a proton to the glycoside bond, respectively. One cation was found to bind to the bottom of the cleft and neutralise the carboxy group of the substrate, decreasing the pKa of the C5 proton to promote catalysis. Our study provides an insight into the structural basis for the catalysis of alginate lyases and beta-helix polysaccharide lyases.

Structural and biochemical characterisation of a novel alginate lyase from Paenibacillus sp. str. FPU-7.,Itoh T, Nakagawa E, Yoda M, Nakaichi A, Hibi T, Kimoto H Sci Rep. 2019 Oct 16;9(1):14870. doi: 10.1038/s41598-019-51006-1. PMID:31619701<ref>PMID:31619701</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6kfn" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Paenibacillus sp. FPU-7]]
[[Category: Hibi T]]
[[Category: Itoh T]]
[[Category: Kimoto H]]
[[Category: Nakagawa E]]
[[Category: Nakaichi A]]
[[Category: Yoda M]]