1q6f: Difference between revisions

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-[[Image:1q6f.gif|left|200px]]
- {{Structure
+==Crystal Structure of Soybean Beta-Amylase Mutant (E178Y) with Increased pH Optimum at pH 7.1==
-|PDB= 1q6f |SIZE=350|CAPTION= <scene name='initialview01'>1q6f</scene>, resolution 2.10&Aring;
+<StructureSection load='1q6f' size='340' side='right'caption='[[1q6f]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
+<table><tr><td colspan='2'>[[1q6f]] is a 1 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=1Q6F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q6F FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2]
+</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>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900005:beta-cellobiose'>PRD_900005</scene>, <scene name='pdbligand=PRD_900018:beta-maltose'>PRD_900018</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-}}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6f OCA], [https://pdbe.org/1q6f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q6f RCSB], [https://www.ebi.ac.uk/pdbsum/1q6f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q6f 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/q6/1q6f_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=1q6f ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Comparison of the architecture around the active site of soybean beta-amylase and Bacillus cereus beta-amylase showed that the hydrogen bond networks (Glu380-(Lys295-Met51) and Glu380-Asn340-Glu178) in soybean beta-amylase around the base catalytic residue, Glu380, seem to contribute to the lower pH optimum of soybean beta-amylase. To convert the pH optimum of soybean beta-amylase (pH 5.4) to that of the bacterial type enzyme (pH 6.7), three mutants of soybean beta-amylase, M51T, E178Y, and N340T, were constructed such that the hydrogen bond networks were removed by site-directed mutagenesis. The kinetic analysis showed that the pH optimum of all mutants shifted dramatically to a neutral pH (range, from 5.4 to 6.0-6.6). The Km values of the mutants were almost the same as that of soybean beta-amylase except in the case of M51T, while the Vmax values of all mutants were low compared with that of soybean beta-amylase. The crystal structure analysis of the wild type-maltose and mutant-maltose complexes showed that the direct hydrogen bond between Glu380 and Asn340 was completely disrupted in the mutants M51T, E178Y, and N340T. In the case of M51T, the hydrogen bond between Glu380 and Lys295 was also disrupted. These results indicated that the reduced pKa value of Glu380 is stabilized by the hydrogen bond network and is responsible for the lower pH optimum of soybean beta-amylase compared with that of the bacterial beta-amylase.
-'''Crystal Structure of Soybean Beta-Amylase Mutant (E178Y) with Increased pH Optimum at pH 7.1'''
+Structural and enzymatic analysis of soybean beta-amylase mutants with increased pH optimum.,Hirata A, Adachi M, Sekine A, Kang YN, Utsumi S, Mikami B J Biol Chem. 2004 Feb 20;279(8):7287-95. Epub 2003 Nov 24. PMID:14638688<ref>PMID:14638688</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1q6f" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Comparison of the architecture around the active site of soybean beta-amylase and Bacillus cereus beta-amylase showed that the hydrogen bond networks (Glu380-(Lys295-Met51) and Glu380-Asn340-Glu178) in soybean beta-amylase around the base catalytic residue, Glu380, seem to contribute to the lower pH optimum of soybean beta-amylase. To convert the pH optimum of soybean beta-amylase (pH 5.4) to that of the bacterial type enzyme (pH 6.7), three mutants of soybean beta-amylase, M51T, E178Y, and N340T, were constructed such that the hydrogen bond networks were removed by site-directed mutagenesis. The kinetic analysis showed that the pH optimum of all mutants shifted dramatically to a neutral pH (range, from 5.4 to 6.0-6.6). The Km values of the mutants were almost the same as that of soybean beta-amylase except in the case of M51T, while the Vmax values of all mutants were low compared with that of soybean beta-amylase. The crystal structure analysis of the wild type-maltose and mutant-maltose complexes showed that the direct hydrogen bond between Glu380 and Asn340 was completely disrupted in the mutants M51T, E178Y, and N340T. In the case of M51T, the hydrogen bond between Glu380 and Lys295 was also disrupted. These results indicated that the reduced pKa value of Glu380 is stabilized by the hydrogen bond network and is responsible for the lower pH optimum of soybean beta-amylase compared with that of the bacterial beta-amylase.
+*[[Amylase 3D structures|Amylase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-Q6F is a [[Single protein]] structure of sequence 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=1Q6F OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Structural and enzymatic analysis of soybean beta-amylase mutants with increased pH optimum., Hirata A, Adachi M, Sekine A, Kang YN, Utsumi S, Mikami B, J Biol Chem. 2004 Feb 20;279(8):7287-95. Epub 2003 Nov 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14638688 14638688]
-[[Category: Beta-amylase]]
 [[Category: Glycine max]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Adachi, M.]]
+[[Category: Adachi M]]
-[[Category: Hirata, A.]]
+[[Category: Hirata A]]
-[[Category: Kang, Y N.]]
+[[Category: Kang YN]]
-[[Category: Mikami, B.]]
+[[Category: Mikami B]]
-[[Category: Sekine, A.]]
+[[Category: Sekine A]]
-[[Category: Utsumi, S.]]
+[[Category: Utsumi S]]
-[[Category: SO4]]
-[[Category: beta-alpha-barrel]]
-[[Category: beta-amylase]]
-[[Category: increased ph optimum]]
-[[Category: maltose complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:33:35 2008''