1vfo: Difference between revisions

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-{{Seed}}
-[[Image:1vfo.png|left|200px]]
-<!--
+==Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/beta-cyclodextrin complex==
-The line below this paragraph, containing "STRUCTURE_1vfo", creates the "Structure Box" on the page.
+<StructureSection load='1vfo' size='340' side='right'caption='[[1vfo]], [[Resolution|resolution]] 2.81&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'>[[1vfo]] 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=1VFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VFO 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]] 2.81&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900012:beta-cyclodextrin'>PRD_900012</scene></td></tr>
-{{STRUCTURE_1vfo|  PDB=1vfo  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vfo OCA], [https://pdbe.org/1vfo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vfo RCSB], [https://www.ebi.ac.uk/pdbsum/1vfo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vfo 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/vf/1vfo_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=1vfo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII) has the unique ability to hydrolyze cyclodextrins (CDs), with various sized cavities, as well as starch. To understand the relationship between structure and substrate specificity, x-ray structures of a TVAII-acarbose complex and inactive mutant TVAII (D325N/D421N)/alpha-, beta- and gamma-CDs complexes were determined at resolutions of 2.9, 2.9, 2.8, and 3.1 A, respectively. In all complexes, the interactions between ligands and enzymes at subsites -1, -2, and -3 were almost the same, but striking differences in the catalytic site structure were found at subsites +1 and +2, where Trp(356) and Tyr(374) changed the conformation of the side chain depending on the structure and size of the ligands. Trp(356) and Tyr(374) are thought to be responsible for the multiple substrate-recognition mechanism of TVAII, providing the unique substrate specificity. In the beta-CD complex, the beta-CD maintains a regular conical structure, making it difficult for Glu(354) to protonate the O-4 atom at the hydrolyzing site as a previously proposed hydrolyzing mechanism of alpha-amylase. From the x-ray structures, it is suggested that the protonation of the O-4 atom is possibly carried out via a hydrogen atom of the inter-glucose hydrogen bond at the hydrolyzing site.
-===Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/beta-cyclodextrin complex===
+Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and cyclodextrins demonstrate the multiple substrate recognition mechanism.,Ohtaki A, Mizuno M, Tonozuka T, Sakano Y, Kamitori S J Biol Chem. 2004 Jul 23;279(30):31033-40. Epub 2004 May 11. PMID:15138257<ref>PMID:15138257</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1vfo" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15138257}}, adds the Publication Abstract to the page
+*[[Amylase 3D structures|Amylase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15138257 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15138257}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VFO is a 2 chains structure with 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=1VFO OCA].
-==Reference==
-<ref group="xtra">PMID:15138257</ref><references group="xtra"/>
-[[Category: Neopullulanase]]
 [[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: Amylase]]
-[[Category: Complex]]
-[[Category: Cyclodextrin]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 22 15:02:47 2010''