View source for 4f13


==Alginate lyase A1-III Y246F complexed with tetrasaccharide==
<StructureSection load='4f13' size='340' side='right'caption='[[4f13]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4f13]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4e25 4e25] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ew4 3ew4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F13 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]] 2.208&#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=MAW:4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC+ACID'>MAW</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=4f13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f13 OCA], [https://pdbe.org/4f13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f13 RCSB], [https://www.ebi.ac.uk/pdbsum/4f13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f13 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9KWU1_SPHSX Q9KWU1_SPHSX] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structures of two mutants (H192A and Y246F) of a mannuronate-specific alginate lyase, A1-III, from Sphingomonas species A1 complexed with a tetrasaccharide substrate [4-deoxy-L-erythro-hex-4-ene-pyranosyluronate-(mannuronate)(2)-mannuronic acid] were determined by X-ray crystallography at around 2.2 A resolution together with the apo form of the H192A mutant. The final models of the complex forms, which comprised two monomers (of 353 amino-acid residues each), 268-287 water molecules and two tetrasaccharide substrates, had R factors of around 0.17. A large conformational change occurred in the position of the lid loop (residues 64-85) in holo H192A and Y246F compared with that in apo H192A. The lid loop migrated about 14 A from an open form to a closed form to interact with the bound tetrasaccharide and a catalytic residue. The tetrasaccharide was bound in the active cleft at subsites -3 to +1 as a substrate form in which the glycosidic linkage to be cleaved existed between subsites -1 and +1. In particular, the O(eta) atom of Tyr68 in the closed lid loop forms a hydrogen bond to the side chain of a presumed catalytic residue, O(eta) of Tyr246, which acts both as an acid and a base catalyst in a syn mechanism.

Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III.,Mikami B, Ban M, Suzuki S, Yoon HJ, Miyake O, Yamasaki M, Ogura K, Maruyama Y, Hashimoto W, Murata K Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1207-16. Epub 2012 Aug 18. PMID:22948922<ref>PMID:22948922</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4f13" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Sphingomonas sp]]
[[Category: Ban M]]
[[Category: Hashimoto W]]
[[Category: Maruyama Y]]
[[Category: Mikami B]]
[[Category: Miyake O]]
[[Category: Murata K]]
[[Category: Ogura K]]
[[Category: Suzuki S]]
[[Category: Yamasaki M]]
[[Category: Yoon H-J]]