2die

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{{Seed}}
 
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[[Image:2die.png|left|200px]]
 
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==Alkaline alpha-amylase AmyK from Bacillus sp. KSM-1378==
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The line below this paragraph, containing "STRUCTURE_2die", creates the "Structure Box" on the page.
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<StructureSection load='2die' size='340' side='right'caption='[[2die]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2die]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._(in:_Bacteria) Bacillus sp. (in: Bacteria)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DIE FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_2die| PDB=2die | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2die FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2die OCA], [https://pdbe.org/2die PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2die RCSB], [https://www.ebi.ac.uk/pdbsum/2die PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2die ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/O82839_BACSP O82839_BACSP]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/di/2die_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2die ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of alkaline liquefying alpha-amylase (AmyK) from the alkaliphilic Bacillus sp. KSM-1378 was determined at 2.1 A resolution. The AmyK structure belongs to the GH13 glycoside hydrolase family, which consists of three domains, and bound three calcium and one sodium ions. The alkaline adaptation mechanism of AmyK was investigated by the ancestral sequence evolutionary trace method and by extensive comparisons between alkaline and nonalkaline enzyme structures, including three other protein families: protease, cellulase, and phosphoserine aminotransferase. The consensus change for the alkaline adaptation process was a decrease in the Lys content. The loss of a Lys residue is associated with ion pair remodeling, which mainly consists of the loss of Lys-Asp/Glu ion pairs and the acquisition of Arg ion pairs, preferably Arg-Glu. The predicted replacements of the positively charged amino acids were often, although not always, used for ion pair remodeling.
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===Alkaline alpha-amylase AmyK from Bacillus sp. KSM-1378===
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Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins.,Shirai T, Igarashi K, Ozawa T, Hagihara H, Kobayashi T, Ozaki K, Ito S Proteins. 2007 Feb 15;66(3):600-10. PMID:17154418<ref>PMID:17154418</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2die" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17154418}}, adds the Publication Abstract to the page
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*[[Amylase 3D structures|Amylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 17154418 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17154418}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2DIE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DIE OCA].
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[[Category: Hagihara H]]
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[[Category: Igarashi K]]
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==Reference==
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[[Category: Ito S]]
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Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins., Shirai T, Igarashi K, Ozawa T, Hagihara H, Kobayashi T, Ozaki K, Ito S, Proteins. 2007 Feb 15;66(3):600-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17154418 17154418]
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[[Category: Kobayashi T]]
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[[Category: Alpha-amylase]]
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[[Category: Ozaki K]]
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[[Category: Bacillus sp.]]
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[[Category: Ozawa T]]
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[[Category: Single protein]]
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[[Category: Shirai T]]
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[[Category: Hagihara, H.]]
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[[Category: Igarashi, K.]]
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[[Category: Ito, S.]]
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[[Category: Kobayashi, T.]]
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[[Category: Ozaki, K.]]
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[[Category: Ozawa, T.]]
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[[Category: Shirai, T.]]
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[[Category: Beta-alpha-barrel]]
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[[Category: Hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 12:08:42 2008''
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Current revision

Alkaline alpha-amylase AmyK from Bacillus sp. KSM-1378

PDB ID 2die

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OCA

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