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2y5e

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BARLEY LIMIT DEXTRINASE IN COMPLEX WITH ALPHA-CYCLODEXTRIN

Structural highlights

2y5e is a 1 chain structure with sequence from Hordeum vulgare. This structure supersedes the now removed PDB entry 2x4c. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.49Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O48541_HORVV

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Vester-Christensen MB, Abou Hachem M, Svensson B, Henriksen A. Crystal structure of an essential enzyme in seed starch degradation: barley limit dextrinase in complex with cyclodextrins. J Mol Biol. 2010 Nov 12;403(5):739-50. Epub 2010 Sep 21. PMID:20863834 doi:10.1016/j.jmb.2010.09.031

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2y5e"

@@ Line 3: / Line 3: @@
 <StructureSection load='2y5e' size='340' side='right'caption='[[2y5e]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2y5e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Barley Barley]. 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>
+<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='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></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.49&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2y4s|2y4s]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pullulanase Pullulanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.41 3.2.1.41] </span></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 ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Barley]]
+[[Category: Hordeum vulgare]]
 [[Category: Large Structures]]
-[[Category: Pullulanase]]
+[[Category: Hachem MA]]
-[[Category: Hachem, M A]]
+[[Category: Henriksen A]]
-[[Category: Henriksen, A]]
+[[Category: Svensson B]]
-[[Category: Svensson, B]]
+[[Category: Vester-Christensen MB]]
-[[Category: Vester-Christensen, M B]]
-[[Category: Debranching enzyme]]
-[[Category: Glycoside hydrolase 13]]
-[[Category: Hydrolase]]
-[[Category: Starch]]

2y5e

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Current revision

BARLEY LIMIT DEXTRINASE IN COMPLEX WITH ALPHA-CYCLODEXTRIN

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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