2d2o: Difference between revisions

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{{Seed}}
[[Image:2d2o.png|left|200px]]


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==Structure of a complex of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with maltohexaose demonstrates the important role of aromatic residues at the reducing end of the substrate binding cleft==
The line below this paragraph, containing "STRUCTURE_2d2o", creates the "Structure Box" on the page.
<StructureSection load='2d2o' size='340' side='right'caption='[[2d2o]], [[Resolution|resolution]] 2.10&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'>[[2d2o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D2O 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]] 2.1&#8491;</td></tr>
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<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=PRD_900035:alpha-maltohexaose'>PRD_900035</scene></td></tr>
{{STRUCTURE_2d2o|  PDB=2d2o  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2o OCA], [https://pdbe.org/2d2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d2o RCSB], [https://www.ebi.ac.uk/pdbsum/2d2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2o ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NEPU2_THEVU NEPU2_THEVU] Hydrolyzes pullulan efficiently but only a small amount of starch. Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Cleaves also (1-6)-alpha-glucosidic linkages to form maltotriose.
== 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/d2/2d2o_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=2d2o ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII) can efficiently hydrolyze both starch and cyclomaltooligosaccharides (cyclodextrins). The crystal structure of an inactive mutant TVAII in a complex with maltohexaose was determined at a resolution of 2.1A. TVAII adopts a dimeric structure to form two catalytic sites, where substrates are found to bind. At the catalytic site, there are many hydrogen bonds between the enzyme and substrate at the non-reducing end from the hydrolyzing site, but few hydrogen bonds at the reducing end, where two aromatic residues, Trp356 and Tyr45, make effective interactions with a substrate. Trp356 drastically changes its side-chain conformation to achieve a strong stacking interaction with the substrate, and Tyr45 from another molecule forms a water-mediated hydrogen bond with the substrate. Kinetic analysis of the wild-type and mutant enzymes in which Trp356 and/or Tyr45 were replaced with Ala suggested that Trp356 and Tyr45 are essential to the catalytic reaction of the enzyme, and that the formation of a dimeric structure is indispensable for TVAII to hydrolyze both starch and cyclodextrins.


===Structure of a complex of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with maltohexaose demonstrates the important role of aromatic residues at the reducing end of the substrate binding cleft===
Structure of a complex of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with maltohexaose demonstrates the important role of aromatic residues at the reducing end of the substrate binding cleft.,Ohtaki A, Mizuno M, Yoshida H, Tonozuka T, Sakano Y, Kamitori S Carbohydr Res. 2006 Jun 12;341(8):1041-6. Epub 2006 Mar 27. PMID:16564038<ref>PMID:16564038</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2d2o" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_16564038}}, adds the Publication Abstract to the page
*[[Amylase 3D structures|Amylase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 16564038 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_16564038}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2D2O is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2O OCA].
 
==Reference==
<ref group="xtra">PMID:16564038</ref><references group="xtra"/>
[[Category: Neopullulanase]]
[[Category: Thermoactinomyces vulgaris]]
[[Category: Thermoactinomyces vulgaris]]
[[Category: Kamitori, S.]]
[[Category: Kamitori S]]
[[Category: Mizuno, M.]]
[[Category: Mizuno M]]
[[Category: Ohtaki, A.]]
[[Category: Ohtaki A]]
[[Category: Sakano, Y.]]
[[Category: Sakano Y]]
[[Category: Tonozuka, T.]]
[[Category: Tonozuka T]]
[[Category: Yoshida, H.]]
[[Category: Yoshida H]]
[[Category: Beta/alpha barrel]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:15:03 2009''
Retrieved from "https://proteopedia.org/2d2o"