1v3l: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1v3l.png|left|200px]]
-<!--
+==Crystal structure of F283L mutant cyclodextrin glycosyltransferase complexed with a pseudo-tetraose derived from acarbose==
-The line below this paragraph, containing "STRUCTURE_1v3l", creates the "Structure Box" on the page.
+<StructureSection load='1v3l' size='340' side='right'caption='[[1v3l]], [[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'>[[1v3l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._1011 Bacillus sp. 1011]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V3L 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>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACI:6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL'>ACI</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GLD:4,6-DIDEOXYGLUCOSE'>GLD</scene></td></tr>
-{{STRUCTURE_1v3l|  PDB=1v3l  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1v3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v3l OCA], [https://pdbe.org/1v3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v3l RCSB], [https://www.ebi.ac.uk/pdbsum/1v3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v3l ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CDGT_BACS0 CDGT_BACS0]
+== 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/v3/1v3l_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=1v3l ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cyclodextrin glycosyltransferase (CGTase) belonging to the alpha-amylase family mainly catalyzes transglycosylation and produces cyclodextrins from starch and related alpha-1,4-glucans. The catalytic site of CGTase specifically conserves four aromatic residues, Phe183, Tyr195, Phe259, and Phe283, which are not found in alpha-amylase. To elucidate the structural role of Phe283, we determined the crystal structures of native and acarbose-complexed mutant CGTases in which Phe283 was replaced with leucine (F283L) or tyrosine (F283Y). The temperature factors of the region 259-269 in native F283L increased &gt;10 A(2) compared with the wild type. The complex formation with acarbose not only increased the temperature factors (&gt;10 A(2)) but also changed the structure of the region 257-267. This region is stabilized by interactions of Phe283 with Phe259 and Leu260 and plays an important role in the cyclodextrin binding. The conformation of the side-chains of Glu257, Phe259, His327, and Asp328 in the catalytic site was altered by the mutation of Phe283 with leucine, and this indicates that Phe283 partly arranges the structure of the catalytic site through contacts with Glu257 and Phe259. The replacement of Phe283 with tyrosine decreased the enzymatic activity in the basic pH range. The hydroxyl group of Tyr283 forms hydrogen bonds with the carboxyl group of Glu257, and the pK(a) of Glu257 in F283Y may be lower than that in the wild type.
-===Crystal structure of F283L mutant cyclodextrin glycosyltransferase complexed with a pseudo-tetraose derived from acarbose===
+Role of Phe283 in enzymatic reaction of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp.1011: Substrate binding and arrangement of the catalytic site.,Kanai R, Haga K, Akiba T, Yamane K, Harata K Protein Sci. 2004 Feb;13(2):457-65. PMID:14739329<ref>PMID:14739329</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1v3l" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14739329}}, adds the Publication Abstract to the page
+*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14739329 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14739329}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[1v3l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp._1011 Bacillus sp. 1011]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V3L OCA].
-==Reference==
-<ref group="xtra">PMID:14739329</ref><ref group="xtra">PMID:14769878</ref><references group="xtra"/>
 [[Category: Bacillus sp. 1011]]
-[[Category: Cyclomaltodextrin glucanotransferase]]
+[[Category: Large Structures]]
-[[Category: Akiba, T.]]
+[[Category: Akiba T]]
-[[Category: Haga, K.]]
+[[Category: Haga K]]
-[[Category: Harata, K.]]
+[[Category: Harata K]]
-[[Category: Kanai, R.]]
+[[Category: Kanai R]]
-[[Category: Yamane, K.]]
+[[Category: Yamane K]]
-[[Category: Acarbose]]
-[[Category: Cgtase]]
-[[Category: Cyclodextrin]]
-[[Category: Transferase]]