1bg9: Difference between revisions

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-{{Seed}}
-[[Image:1bg9.png|left|200px]]
-<!--
+==BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE==
-The line below this paragraph, containing "STRUCTURE_1bg9", creates the "Structure Box" on the page.
+<StructureSection load='1bg9' size='340' side='right'caption='[[1bg9]], [[Resolution|resolution]] 2.80&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'>[[1bg9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BG9 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]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AF1:4,6-DIDEOXY-4-{[(1S,4S,5S,6S)-4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}-BETA-D-GLUCOPYRANOSE'>AF1</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAF:4,6-DIDEOXY-4-{[(1S,5R,6S)-3-FORMYL-5,6-DIHYDROXY-4-OXOCYCLOHEX-2-EN-1-YL]AMINO}-ALPHA-D-XYLO-HEX-5-ENOPYRANOSE'>DAF</scene></td></tr>
-{{STRUCTURE_1bg9|  PDB=1bg9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bg9 OCA], [https://pdbe.org/1bg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bg9 RCSB], [https://www.ebi.ac.uk/pdbsum/1bg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bg9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMY2_HORVU AMY2_HORVU]
+== 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/bg/1bg9_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=1bg9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+alpha-Amylases are widely occurring, multidomain proteins with a catalytic (beta/alpha)8-barrel. In barley alpha-amylase, insight into the catalytic mechanism is gained from the X-ray crystal structure of its molecular complex with acarbose, a pseudotetrasaccharide that acts like a transition-state analogue and which is shown to bind at two specific regions of the enzyme. The structure of the complex has been refined to an R-factor of 15.1% for all observations with Fo&gt;sigma(Fo) between 10 and 2.8 A resolution. A difference Fourier map produced after refinement of the native structure against the data of the acarbose complex clearly revealed density corresponding to two oligosaccharide-binding sites. One of these is defined as the surface-located starch granule-binding site characteristic of cereal alpha-amylases. It involves stacking of two acarbose rings on Trp276 and Trp277. The other binding region is the active site covering subsites -1, +1 and +2. Here, Glu204 is positioned to act in general acid/base catalysis protonating the glucosidic oxygen atom assisted by Asp289. A water molecule that bridges Glu204 and Asp289 is found at the entrance cavity containing a total of five water molecules. This water molecule is proposed to reprotonate Glu204 and supply the hydroxyl ion for nucleophilic attack on the glucosyl C1 atom. Asp 179 acts as the nucleophile that can bind covalently to the substrate intermediate after bond cleavage. The present complex structure together with the conservation of active-site residues among alpha-amylases and related enzymes, are consistent with a common catalytic mechanism for this class of retaining carbohydrases.
-===BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE===
+Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis.,Kadziola A, Sogaard M, Svensson B, Haser R J Mol Biol. 1998 Apr 24;278(1):205-17. PMID:9571044<ref>PMID:9571044</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1bg9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9571044}}, adds the Publication Abstract to the page
+*[[Amylase 3D structures|Amylase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9571044 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9571044}}
+__TOC__
+</StructureSection>
-==About this Structure==
-BG9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BG9 OCA].
-==Reference==
-Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis., Kadziola A, Sogaard M, Svensson B, Haser R, J Mol Biol. 1998 Apr 24;278(1):205-17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9571044 9571044]
-[[Category: Alpha-amylase]]
 [[Category: Hordeum vulgare]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Haser, R.]]
+[[Category: Haser R]]
-[[Category: Kadziola, A.]]
+[[Category: Kadziola A]]
-[[Category: Hydrolase]]
-[[Category: O-glycosyl]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 19:05:56 2008''