1pez: Difference between revisions

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-{{Seed}}
-[[Image:1pez.png|left|200px]]
-<!--
+==Bacillus circulans strain 251 mutant A230V==
-The line below this paragraph, containing "STRUCTURE_1pez", creates the "Structure Box" on the page.
+<StructureSection load='1pez' size='340' side='right'caption='[[1pez]], [[Resolution|resolution]] 2.32&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'>[[1pez]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Niallia_circulans Niallia circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PEZ 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]] 2.32&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</scene>, <scene name='pdbligand=PRD_900009:alpha-maltotriose'>PRD_900009</scene>, <scene name='pdbligand=PRD_900018:beta-maltose'>PRD_900018</scene></td></tr>
-{{STRUCTURE_1pez|  PDB=1pez  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pez OCA], [https://pdbe.org/1pez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pez RCSB], [https://www.ebi.ac.uk/pdbsum/1pez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pez ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CDGT2_NIACI CDGT2_NIACI]
+== 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/pe/1pez_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=1pez ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cyclodextrin glycosyltransferase (CGTase) preferably catalyzes transglycosylation reactions, whereas many other alpha-amylase family enzymes are hydrolases. Despite the availability of three-dimensional structures of several transglycosylases and hydrolases of this family, the factors that determine the hydrolysis and transglycosylation specificity are far from understood. To identify the amino acid residues that are critical for the transglycosylation reaction specificity, we carried out error-prone PCR mutagenesis and screened for Bacillus circulans strain 251 CGTase mutants with increased hydrolytic activity. After three rounds of mutagenesis the hydrolytic activity had increased 90-fold, reaching the highest hydrolytic activity ever reported for a CGTase. The single mutation with the largest effect (A230V) occurred in a residue not studied before. The structure of this A230V mutant suggests that the larger valine side chain hinders substrate binding at acceptor subsite +1, although not to the extent that catalysis is impossible. The much higher hydrolytic than transglycosylation activity of this mutant indicates that the use of sugar acceptors is hindered especially. This observation is in favor of a proposed induced-fit mechanism, in which sugar acceptor binding at acceptor subsite +1 activates the enzyme in transglycosylation [Uitdehaag et al. (2000) Biochemistry 39, 7772-7780]. As the A230V mutation introduces steric hindrance at subsite +1, this mutation is expected to negatively affect the use of sugar acceptors. Thus, the characteristics of mutant A230V strongly support the existence of the proposed induced-fit mechanism in which sugar acceptor binding activates CGTase in a transglycosylation reaction.
-===Bacillus circulans strain 251 mutant A230V===
+Conversion of cyclodextrin glycosyltransferase into a starch hydrolase by directed evolution: the role of alanine 230 in acceptor subsite +1.,Leemhuis H, Rozeboom HJ, Wilbrink M, Euverink GJ, Dijkstra BW, Dijkhuizen L Biochemistry. 2003 Jun 24;42(24):7518-26. PMID:12809508<ref>PMID:12809508</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1pez" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12809508}}, adds the Publication Abstract to the page
+*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12809508 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12809508}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-PEZ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_circulans Bacillus circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEZ OCA].
+[[Category: Niallia circulans]]
+[[Category: Dijkstra BW]]
-==Reference==
+[[Category: Rozeboom HJ]]
-<ref group="xtra">PMID:12809508</ref><references group="xtra"/>
-[[Category: Bacillus circulans]]
-[[Category: Cyclomaltodextrin glucanotransferase]]
-[[Category: Dijkstra, B W.]]
-[[Category: Rozeboom, H J.]]
-[[Category: Cyclodextrin]]
-[[Category: Glycosyltransferase]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 22 14:55:52 2010''