3gd9: Difference between revisions

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New page: '''Unreleased structure''' The entry 3gd9 is ON HOLD Authors: Wu, H.M., Hsu, M.T., Liu, S.W., Lai, C.C., Hung, C.L., Li, Y.K., Wang, W.C. Description: Crystal structure of laminaripent...
 
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'''Unreleased structure'''


The entry 3gd9 is ON HOLD
==Crystal structure of laminaripentaose-producing beta-1,3-glucanase in complex with laminaritetraose==
<StructureSection load='3gd9' size='340' side='right'caption='[[3gd9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3gd9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_matensis Streptomyces matensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GD9 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]] 1.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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=3gd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gd9 OCA], [https://pdbe.org/3gd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gd9 RCSB], [https://www.ebi.ac.uk/pdbsum/3gd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gd9 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9Z4I2_9ACTN Q9Z4I2_9ACTN]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/3gd9_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3gd9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Laminaripentaose-producing beta-1,3-glucanase (LPHase), a member of glycoside hydrolase family 64, cleaves a long-chain polysaccharide beta-1,3-glucan into specific pentasaccharide oligomers. The crystal structure of LPHase from Streptomyces matensis DIC-108 was solved to 1.62 A resolution using multiple-wavelength anomalous dispersion methods. The LPHase structure reveals a novel crescent-like fold; it consists of a barrel domain and a mixed (alpha/beta) domain, forming a wide-open groove between the two domains. The liganded crystal structure was also solved to 1.80 A, showing limited conformational changes. Within the wide groove, a laminaritetraose molecule is found to sit in an electronegatively charged central region and is proximal to several conserved residues including two carboxylates (Glu(154) and Asp(170)) and four other sugar-binding residues (Thr(156), Asn(158), Trp(163), and Thr(167)). Molecular modeling using a laminarihexaose as a substrate suggests roles for Glu(154) and Asp(170) as acid and base catalysts, respectively, whereas the side chains of Thr(156), Asn(158), and Trp(163) demarcate subsite +5. Site-directed mutagenesis of Glu(154) and Asp(170) confirms that both carboxylates are essential for catalysis. Together, our results suggest that LPHase uses a direct displacement mechanism involving Glu(154) and Asp(170) to cleave a beta-1,3-glucan into specific alpha-pentasaccharide oligomers.


Authors: Wu, H.M., Hsu, M.T., Liu, S.W., Lai, C.C., Hung, C.L., Li, Y.K., Wang, W.C.
Structure, mechanistic action, and essential residues of a GH-64 enzyme, laminaripentaose-producing beta-1,3-glucanase.,Wu HM, Liu SW, Hsu MT, Hung CL, Lai CC, Cheng WC, Wang HJ, Li YK, Wang WC J Biol Chem. 2009 Sep 25;284(39):26708-15. Epub 2009 Jul 29. PMID:19640850<ref>PMID:19640850</ref>


Description: Crystal structure of laminaripentaose-producing beta-1,3-glucanase in complex with laminaritetraose
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3gd9" style="background-color:#fffaf0;"></div>


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 11 11:11:21 2009''
==See Also==
*[[Glucanase 3D structures|Glucanase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Streptomyces matensis]]
[[Category: Hsu MT]]
[[Category: Lai CC]]
[[Category: Li YK]]
[[Category: Liu SW]]
[[Category: Wang WC]]
[[Category: Wu HM]]
Retrieved from "https://proteopedia.org/3gd9"