2y5e: Difference between revisions
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New page: '''Unreleased structure''' The entry 2y5e is ON HOLD Authors: VESTER-CHRISTENSEN, M.B., HACHEM, M.A., SVENSSON, B., HENRIKSEN, A. Description: BARLEY LIMIT DEXTRINASE IN COMPLEX WITH A... |
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==BARLEY LIMIT DEXTRINASE IN COMPLEX WITH ALPHA-CYCLODEXTRIN== | |||
<StructureSection load='2y5e' size='340' side='right'caption='[[2y5e]], [[Resolution|resolution]] 2.49Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2y5e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2x4c 2x4c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y5E 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]] 2.49Å</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PRD_900015:alpha-cyclodextrin'>PRD_900015</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=2y5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y5e OCA], [https://pdbe.org/2y5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y5e RCSB], [https://www.ebi.ac.uk/pdbsum/2y5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y5e ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/O48541_HORVV O48541_HORVV] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Barley limit dextrinase [Hordeum vulgare limit dextrinase (HvLD)] catalyzes the hydrolysis of alpha-1,6 glucosidic linkages in limit dextrins. This activity plays a role in starch degradation during germination and presumably in starch biosynthesis during grain filling. The crystal structures of HvLD in complex with the competitive inhibitors alpha-cyclodextrin (CD) and beta-CD are solved and refined to 2.5 A and 2.1 A, respectively, and are the first structures of a limit dextrinase. HvLD belongs to glycoside hydrolase 13 family and is composed of four domains: an immunoglobulin-like N-terminal eight-stranded beta-sandwich domain, a six-stranded beta-sandwich domain belonging to the carbohydrate binding module 48 family, a catalytic (beta/alpha)(8)-like barrel domain that lacks alpha-helix 5, and a C-terminal eight-stranded beta-sandwich domain of unknown function. The CDs are bound at the active site occupying carbohydrate binding subsites +1 and +2. A glycerol and three water molecules mimic a glucose residue at subsite -1, thereby identifying residues involved in catalysis. The bulky Met440, a unique residue at its position among alpha-1,6 acting enzymes, obstructs subsite -4. The steric hindrance observed is proposed to affect substrate specificity and to cause a low activity of HvLD towards amylopectin. An extended loop (Asp513-Asn520) between beta5 and beta6 of the catalytic domain also seems to influence substrate specificity and to give HvLD a higher affinity for alpha-CD than pullulanases. The crystal structures additionally provide new insight into cation sites and the concerted action of the battery of hydrolytic enzymes in starch degradation. | |||
Crystal structure of an essential enzyme in seed starch degradation: barley limit dextrinase in complex with cyclodextrins.,Vester-Christensen MB, Abou Hachem M, Svensson B, Henriksen A J Mol Biol. 2010 Nov 12;403(5):739-50. Epub 2010 Sep 21. PMID:20863834<ref>PMID:20863834</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2y5e" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Hordeum vulgare]] | |||
[[Category: Large Structures]] | |||
[[Category: Hachem MA]] | |||
[[Category: Henriksen A]] | |||
[[Category: Svensson B]] | |||
[[Category: Vester-Christensen MB]] | |||
