4j3x: Difference between revisions

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~~'''Unreleased structure'''~~

The ~~entry 4j3x~~ is ~~ON HOLD~~

==Crystal structure of barley limit dextrinase (E510A mutant) in complex with a branched maltoheptasaccharide==

== Structural highlights ==

<table><tr><td colspan='2'>[[4j3x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J3X 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]] 1.75Å</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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=4j3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j3x OCA], [https://pdbe.org/4j3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j3x RCSB], [https://www.ebi.ac.uk/pdbsum/4j3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j3x ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/Q9FYY0_HORVU Q9FYY0_HORVU]

== Publication Abstract from PubMed ==

Complete hydrolytic degradation of starch requires hydrolysis of both the alpha-1,4- and alpha-1,6-glucosidic bonds in amylopectin. Limit dextrinase (LD) is the only endogenous barley enzyme capable of hydrolyzing the alpha-1,6-glucosidic bond during seed germination, and impaired LD activity inevitably reduces the maltose and glucose yields from starch degradation. Crystal structures of barley LD and active-site mutants with natural substrates, products and substrate analogues were sought to better understand the facets of LD-substrate interactions that confine high activity of LD to branched maltooligosaccharides. For the first time, an intact alpha-1,6-glucosidically linked substrate spanning the active site of a LD or pullulanase has been trapped and characterized by crystallography. The crystal structure reveals both the branch and main-chain binding sites and is used to suggest a mechanism for nucleophilicity enhancement in the active site. The substrate, product and analogue complexes were further used to outline substrate binding subsites and substrate binding restraints and to suggest a mechanism for avoidance of dual alpha-1,6- and alpha-1,4-hydrolytic activity likely to be a biological necessity during starch synthesis.

~~Authors:~~ Sim, L., ~~Windahl~~, M.S, ~~Moeller~~, M.S., ~~Henriksen, A~~.

Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase.,Moller MS, Windahl MS, Sim L, Bojstrup M, Abou Hachem M, Hindsgaul O, Palcic M, Svensson B, Henriksen A J Mol Biol. 2015 Mar 27;427(6 Pt B):1263-77. doi: 10.1016/j.jmb.2014.12.019. Epub, 2015 Jan 3. PMID:25562209<ref>PMID:25562209</ref>

~~Description~~: ~~Crystal structure of barley limit dextrinase (E510A mutant) in complex with a branched maltoheptasaccharide~~

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

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Hordeum vulgare]]

[[Category: Large Structures]]

[[Category: Henriksen A]]

[[Category: Moeller MS]]

[[Category: Sim L]]

[[Category: Windahl MS]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 4j3x is ON HOLD
+==Crystal structure of barley limit dextrinase (E510A mutant) in complex with a branched maltoheptasaccharide==
+<StructureSection load='4j3x' size='340' side='right'caption='[[4j3x]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4j3x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J3X 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]] 1.75&#8491;</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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=4j3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j3x OCA], [https://pdbe.org/4j3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j3x RCSB], [https://www.ebi.ac.uk/pdbsum/4j3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j3x ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9FYY0_HORVU Q9FYY0_HORVU]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Complete hydrolytic degradation of starch requires hydrolysis of both the alpha-1,4- and alpha-1,6-glucosidic bonds in amylopectin. Limit dextrinase (LD) is the only endogenous barley enzyme capable of hydrolyzing the alpha-1,6-glucosidic bond during seed germination, and impaired LD activity inevitably reduces the maltose and glucose yields from starch degradation. Crystal structures of barley LD and active-site mutants with natural substrates, products and substrate analogues were sought to better understand the facets of LD-substrate interactions that confine high activity of LD to branched maltooligosaccharides. For the first time, an intact alpha-1,6-glucosidically linked substrate spanning the active site of a LD or pullulanase has been trapped and characterized by crystallography. The crystal structure reveals both the branch and main-chain binding sites and is used to suggest a mechanism for nucleophilicity enhancement in the active site. The substrate, product and analogue complexes were further used to outline substrate binding subsites and substrate binding restraints and to suggest a mechanism for avoidance of dual alpha-1,6- and alpha-1,4-hydrolytic activity likely to be a biological necessity during starch synthesis.
-Authors: Sim, L., Windahl, M.S, Moeller, M.S., Henriksen, A.
+Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase.,Moller MS, Windahl MS, Sim L, Bojstrup M, Abou Hachem M, Hindsgaul O, Palcic M, Svensson B, Henriksen A J Mol Biol. 2015 Mar 27;427(6 Pt B):1263-77. doi: 10.1016/j.jmb.2014.12.019. Epub, 2015 Jan 3. PMID:25562209<ref>PMID:25562209</ref>
-Description: Crystal structure of barley limit dextrinase (E510A mutant) in complex with a branched maltoheptasaccharide
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4j3x" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Hordeum vulgare]]
+[[Category: Large Structures]]
+[[Category: Henriksen A]]
+[[Category: Moeller MS]]
+[[Category: Sim L]]
+[[Category: Windahl MS]]