1uko: Difference between revisions

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-{{Seed}}
-[[Image:1uko.png|left|200px]]
-<!--
+==Crystal structure of soybean beta-amylase mutant substituted at surface region==
-The line below this paragraph, containing "STRUCTURE_1uko", creates the "Structure Box" on the page.
+<StructureSection load='1uko' size='340' side='right'caption='[[1uko]], [[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'>[[1uko]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UKO 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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1uko|  PDB=1uko  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1uko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uko OCA], [https://pdbe.org/1uko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uko RCSB], [https://www.ebi.ac.uk/pdbsum/1uko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uko ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMYB_SOYBN AMYB_SOYBN]
+== 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/1uko_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=1uko ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In spite of the high similarity of amino acid sequence and three-dimensional structure between soybean beta-amylase (SBA) and sweet potato beta-amylase (SPB), their quaternary structure is quite different, being a monomer in SBA and a tetramer in SPB. Because most of the differences in amino acid sequences are found in the surface region, we tested the tetramerization of SBA by examining mutations of residues located at the surface. We designed the SBA tetramer using the SPB tetramer structure as a model and calculating the change of accessible surface area (DeltaASA) for each residue in order to select sites for the mutation. Two different mutant genes encoding SB3 (D374Y/L481R/P487D) and SB4 (K462S added to SB3), were constructed for expression in Escherichia coli and the recombinant proteins were purified. They existed as a monomer in solution, but gave completely different crystals from the native SBA. The asymmetric unit of the mutants contains four molecules, while that of native SBA contains one. The interactions of the created interfaces revealed that there were more intermolecular interactions in the SB3 than in the SB4 tetramer. The substituted charged residues on the surface are involved in interactions with adjacent molecules in a different way, forming a new crystal packing pattern.
-===Crystal structure of soybean beta-amylase mutant substituted at surface region===
+Change in the crystal packing of soybean beta-amylase mutants substituted at a few surface amino acid residues.,Kang YN, Adachi M, Mikami B, Utsumi S Protein Eng. 2003 Nov;16(11):809-17. PMID:14631070<ref>PMID:14631070</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1uko" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14631070}}, adds the Publication Abstract to the page
+*[[Amylase 3D structures|Amylase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14631070 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14631070}}
+__TOC__
+</StructureSection>
-==About this Structure==
-UKO is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKO OCA].
-==Reference==
-<ref group="xtra">PMID:14631070</ref><references group="xtra"/>
-[[Category: Beta-amylase]]
 [[Category: Glycine max]]
-[[Category: Adachi, M.]]
+[[Category: Large Structures]]
-[[Category: Kang, Y N.]]
+[[Category: Adachi M]]
-[[Category: Mikami, B.]]
+[[Category: Kang YN]]
-[[Category: Utsumi, S.]]
+[[Category: Mikami B]]
+[[Category: Utsumi S]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:09:34 2009''