2v8l: Difference between revisions

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{{Seed}}
[[Image:2v8l.png|left|200px]]


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==Carbohydrate-binding of the starch binding domain of Rhizopus oryzae glucoamylase in complex with beta-cyclodextrin and maltoheptaose==
The line below this paragraph, containing "STRUCTURE_2v8l", creates the "Structure Box" on the page.
<StructureSection load='2v8l' size='340' side='right'caption='[[2v8l]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2v8l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhizopus_arrhizus Rhizopus arrhizus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V8L FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900012:beta-cyclodextrin'>PRD_900012</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
{{STRUCTURE_2v8l|  PDB=2v8l  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v8l OCA], [https://pdbe.org/2v8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v8l RCSB], [https://www.ebi.ac.uk/pdbsum/2v8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v8l ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/B7XC04_RHIOR B7XC04_RHIOR]
== 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/v8/2v8l_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=2v8l ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
GA (glucoamylase) hydrolyses starch and polysaccharides to beta-D-glucose. RoGA (Rhizopus oryzae GA) consists of two functional domains, an N-terminal SBD (starch-binding domain) and a C-terminal catalytic domain, which are connected by an O-glycosylated linker. In the present study, the crystal structures of the SBD from RoGA (RoGACBM21) and the complexes with beta-cyclodextrin (SBD-betaCD) and maltoheptaose (SBD-G7) were determined. Two carbohydrate binding sites, I (Trp(47)) and II (Tyr(32)), were resolved and their binding was co-operative. Besides the hydrophobic interaction, two unique polyN loops comprising consecutive asparagine residues also participate in the sugar binding. A conformational change in Tyr(32) was observed between unliganded and liganded SBDs. To elucidate the mechanism of polysaccharide binding, a number of mutants were constructed and characterized by a quantitative binding isotherm and Scatchard analysis. A possible binding path for long-chain polysaccharides in RoGACBM21 was proposed.


===CARBOHYDRATE-BINDING OF THE STARCH BINDING DOMAIN OF RHIZOPUS ORYZAE GLUCOAMYLASE IN COMPLEX WITH BETA-CYCLODEXTRIN AND MALTOHEPTAOSE===
Crystal structures of the starch-binding domain from Rhizopus oryzae glucoamylase reveal a polysaccharide-binding path.,Tung JY, Chang MD, Chou WI, Liu YY, Yeh YH, Chang FY, Lin SC, Qiu ZL, Sun YJ Biochem J. 2008 Nov 15;416(1):27-36. PMID:18588504<ref>PMID:18588504</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
2V8L is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rhizopus_oryzae Rhizopus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V8L OCA].
<div class="pdbe-citations 2v8l" style="background-color:#fffaf0;"></div>
[[Category: Glucan 1,4-alpha-glucosidase]]
== References ==
[[Category: Rhizopus oryzae]]
<references/>
[[Category: Liu, Y Y.]]
__TOC__
[[Category: Sun, Y J.]]
</StructureSection>
[[Category: Tung, J Y.]]
[[Category: Large Structures]]
[[Category: Beta-cyclodextrin]]
[[Category: Rhizopus arrhizus]]
[[Category: Carbohydrate binding]]
[[Category: Liu Y-Y]]
[[Category: Hydrolase]]
[[Category: Sun Y-J]]
[[Category: Maltoheptaose]]
[[Category: Tung J-Y]]
[[Category: Rhizopus oryzae glucoamylase]]
[[Category: Starch binding domain]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:00:19 2009''

Latest revision as of 15:09, 13 December 2023

Carbohydrate-binding of the starch binding domain of Rhizopus oryzae glucoamylase in complex with beta-cyclodextrin and maltoheptaose

2v8l, resolution 1.80Å

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