1itc: Difference between revisions

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-{{Seed}}
-[[Image:1itc.png|left|200px]]
-<!--
+==Beta-Amylase from Bacillus cereus var. mycoides Complexed with Maltopentaose==
-The line below this paragraph, containing "STRUCTURE_1itc", creates the "Structure Box" on the page.
+<StructureSection load='1itc' size='340' side='right'caption='[[1itc]], [[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'>[[1itc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ITC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ITC 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=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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_900010:alpha-maltotetraose'>PRD_900010</scene>, <scene name='pdbligand=PRD_900030:alpha-maltopentaose'>PRD_900030</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1itc|  PDB=1itc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1itc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1itc OCA], [https://pdbe.org/1itc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1itc RCSB], [https://www.ebi.ac.uk/pdbsum/1itc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1itc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMYB_BACCE AMYB_BACCE]
+== 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/it/1itc_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=1itc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The X-ray crystal structure of a catalytic site mutant of beta-amylase, E172A (Glu172 --&gt; Ala), from Bacillus cereus var. mycoides complexed with a substrate, maltopentaose (G5), and the wild-type enzyme complexed with maltose were determined at 2.1 and 2.0 A resolution, respectively. Clear and continuous density corresponding to G5 was observed in the active site of E172A, and thus, the substrate, G5, was not hydrolyzed. All glucose residues adopted a relaxed (4)C(1) conformation, and the conformation of the maltose unit for Glc2 and Glc3 was much different from those of other maltose units, where each glucose residue of G5 is named Glc1-Glc5 (Glc1 is at the nonreducing end). A water molecule was observed 3.3 A from the C1 atom of Glc2, and 3.0 A apart from the OE1 atom of Glu367 which acts as a general base. In the wild-type enzyme-maltose complex, two maltose molecules bind at subsites -2 and -1 and at subsites +1 and +2 in tandem. The conformation of the maltose molecules was similar to that of the condensation product of soybean beta-amylase, but differed from that of G5 in E172A. When the substrate flips between Glc2 and Glc3, the conformational energy of the maltose unit was calculated to be 20 kcal/mol higher than that of the cis conformation by MM3. We suggest that beta-amylase destabilizes the bond that is to be broken in the ES complex, decreasing the activation energy, DeltaG(++), which is the difference in free energy between this state and the transition state.
-===Beta-Amylase from Bacillus cereus var. mycoides Complexed with Maltopentaose===
+Crystal structure of a catalytic site mutant of beta-amylase from Bacillus cereus var. mycoides cocrystallized with maltopentaose.,Miyake H, Kurisu G, Kusunoki M, Nishimura S, Kitamura S, Nitta Y Biochemistry. 2003 May 20;42(19):5574-81. PMID:12741813<ref>PMID:12741813</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1itc" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12741813}}, adds the Publication Abstract to the page
+*[[Amylase 3D structures|Amylase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12741813 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12741813}}
+__TOC__
+</StructureSection>
-==About this Structure==
-ITC is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ITC OCA].
-==Reference==
-<ref group="xtra">PMID:12741813</ref><references group="xtra"/>
 [[Category: Bacillus cereus]]
-[[Category: Beta-amylase]]
+[[Category: Large Structures]]
-[[Category: Kitamura, S.]]
+[[Category: Kitamura S]]
-[[Category: Kurisu, G.]]
+[[Category: Kurisu G]]
-[[Category: Kusunoki, M.]]
+[[Category: Kusunoki M]]
-[[Category: Miyake, H.]]
+[[Category: Miyake H]]
-[[Category: Nishimura, S.]]
+[[Category: Nishimura S]]
-[[Category: Nitta, Y.]]
+[[Category: Nitta Y]]
-[[Category: Beta-amylase]]
-[[Category: Catalytic-site mutant]]
-[[Category: Hydrolase]]
-[[Category: Maltopentaose]]
-[[Category: Raw-starch binding domain]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:14:11 2009''