2vq4: Difference between revisions

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{{Seed}}
[[Image:2vq4.jpg|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_2vq4", creates the "Structure Box" on the page.
<StructureSection load='2vq4' size='340' side='right'caption='[[2vq4]], [[Resolution|resolution]] 1.25&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'>[[2vq4]] 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=2VQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VQ4 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]] 1.25&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vq4 OCA], [https://pdbe.org/2vq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vq4 RCSB], [https://www.ebi.ac.uk/pdbsum/2vq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vq4 ProSAT]</span></td></tr>
{{STRUCTURE_2vq4|  PDB=2vq4  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q2VC81_RHIOR Q2VC81_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/vq/2vq4_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=2vq4 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>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_18588504}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2vq4" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 18588504 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18588504}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2VQ4 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=2VQ4 OCA].
[[Category: Rhizopus arrhizus]]
 
[[Category: Liu Y-Y]]
==Reference==
[[Category: Sun Y-J]]
<ref group="xtra">PMID:18588504</ref><references group="xtra"/>
[[Category: Tung J-Y]]
[[Category: Glucan 1,4-alpha-glucosidase]]
[[Category: Rhizopus oryzae]]
[[Category: Liu, Y Y.]]
[[Category: Sun, Y J.]]
[[Category: Tung, J Y.]]
[[Category: Carbohydrate binding]]
[[Category: Hydrolase]]
[[Category: Rhizopus oryzae glucoamylase]]
[[Category: Starch binding domain]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  8 09:29:08 2009''

Latest revision as of 15:28, 13 December 2023

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

2vq4, resolution 1.25Å

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