1uks: Difference between revisions

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-{{Seed}}
-[[Image:1uks.png|left|200px]]
-<!--
+==Crystal structure of F183L/F259L mutant cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose==
-The line below this paragraph, containing "STRUCTURE_1uks", creates the "Structure Box" on the page.
+<StructureSection load='1uks' size='340' side='right'caption='[[1uks]], [[Resolution|resolution]] 1.90&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'>[[1uks]] 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=1UKS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UKS 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]] 1.9&#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_1uks|  PDB=1uks  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1uks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uks OCA], [https://pdbe.org/1uks PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uks RCSB], [https://www.ebi.ac.uk/pdbsum/1uks PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uks 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/uk/1uks_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1uks ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The stacking interaction between a tyrosine residue and the sugar ring at the catalytic subsite -1 is strictly conserved in the glycoside hydrolase family 13 enzymes. Replacing Tyr100 with leucine in cyclodextrin glycosyltransferase (CGTase) from Bacillus sp. 1011 to prevent stacking significantly decreased all CGTase activities. The adjacent stacking interaction with both Phe183 and Phe259 onto the sugar ring at subsite +2 is essentially conserved among CGTases. F183L/F259L mutant CGTase affects donor substrate binding and/or acceptor binding during transglycosylation [Nakamura et al. (1994) Biochemistry 33, 9929-9936]. To elucidate the precise role of carbohydrate/aromatic stacking interaction at subsites -1 and +2 on the substrate binding of CGTases, we analyzed the X-ray structures of wild-type (2.0 A resolution), and Y100L (2.2 A resolution) and F183L/F259L mutant (1.9 A resolution) CGTases complexed with the inhibitor, acarbose. The refined structures revealed that acarbose molecules bound to the Y100L mutant moved from the active center toward the side chain of Tyr195, and the hydrogen bonding and hydrophobic interaction between acarbose and subsites significantly diminished. The position of pseudo-tetrasaccharide binding in the F183L/F259L mutant was closer to the non-reducing end, and the torsion angles of glycosidic linkages at subsites -1 to +1 on molecule 1 and subsites -2 to -1 on molecule 2 significantly changed compared with that of each molecule of wild-type-acarbose complex to adopt the structural change of subsite +2. These structural and biochemical data suggest that substrate binding in the active site of CGTase is critically affected by the carbohydrate/aromatic stacking interaction with Tyr100 at the catalytic subsite -1 and that this effect is likely a result of cooperation between Tyr100 and Phe259 through stacking interaction with substrate at subsite +2.
-===Crystal structure of F183L/F259L mutant cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose===
+Effects of essential carbohydrate/aromatic stacking interaction with Tyr100 and Phe259 on substrate binding of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp. 1011.,Haga K, Kanai R, Sakamoto O, Aoyagi M, Harata K, Yamane K J Biochem. 2003 Dec;134(6):881-91. PMID:14769878<ref>PMID:14769878</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1uks" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14769878}}, adds the Publication Abstract to the page
+*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14769878 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14769878}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bacillus sp. 1011]]
-UKS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKS OCA].
+[[Category: Large Structures]]
+[[Category: Haga K]]
-==Reference==
+[[Category: Harata K]]
-Effects of essential carbohydrate/aromatic stacking interaction with Tyr100 and Phe259 on substrate binding of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp. 1011., Haga K, Kanai R, Sakamoto O, Aoyagi M, Harata K, Yamane K, J Biochem. 2003 Dec;134(6):881-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14769878 14769878]
+[[Category: Kanai R]]
-[[Category: Bacillus sp.]]
+[[Category: Sakamoto O]]
-[[Category: Cyclomaltodextrin glucanotransferase]]
+[[Category: Yamane K]]
-[[Category: Single protein]]
-[[Category: Haga, K.]]
-[[Category: Harata, K.]]
-[[Category: Kanai, R.]]
-[[Category: Sakamoto, O.]]
-[[Category: Yamane, K.]]
-[[Category: Acarbose]]
-[[Category: Carbohydrate/protein interaction]]
-[[Category: Cgtase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 12:28:33 2008''