1ud2

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{{Seed}}
 
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[[Image:1ud2.png|left|200px]]
 
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==Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38)==
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The line below this paragraph, containing "STRUCTURE_1ud2", creates the "Structure Box" on the page.
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<StructureSection load='1ud2' size='340' side='right'caption='[[1ud2]], [[Resolution|resolution]] 2.13&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'>[[1ud2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._KSM-K38 Bacillus sp. KSM-K38]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UD2 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]] 2.13&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_1ud2| PDB=1ud2 | 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=1ud2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ud2 OCA], [https://pdbe.org/1ud2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ud2 RCSB], [https://www.ebi.ac.uk/pdbsum/1ud2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ud2 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q93I48_9BACI Q93I48_9BACI]
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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/ud/1ud2_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=1ud2 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 a calcium-free alpha-amylase (AmyK38) from Bacillus sp. strain KSM-K38, which resists chelating reagents and chemical oxidants, has been determined by the molecular replacement method and refined to a crystallographic R-factor of 19.9% (R-free of 23.2%) at 2.13-A resolution. The main chain folding of AmyK38 is almost homologous to that of Bacillus licheniformis alpha-amylase. However, neither a highly conserved calcium ion, which is located at the interface between domains A and B, nor any other calcium ions appear to exist in the AmyK38 molecule, although three sodium ions were found, one of which is located at the position corresponding to that of a highly conserved calcium ion of other alpha-amylases. The existence of these sodium ions was crystallographically confirmed by the structures of three metal-exchanged and mutated enzymes. This is the first case in which the structure of the calcium-free alpha-amylase has been determined by crystallography, and it was suggested that these sodium ions, instead of calcium ions, are used to retain the structure and function of AmyK38.
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===Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38)===
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Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites.,Nonaka T, Fujihashi M, Kita A, Hagihara H, Ozaki K, Ito S, Miki K J Biol Chem. 2003 Jul 4;278(27):24818-24. Epub 2003 Apr 28. PMID:12719434<ref>PMID:12719434</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 1ud2" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_12719434}}, 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 12719434 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12719434}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Bacillus sp. KSM-K38]]
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1UD2 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UD2 OCA].
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[[Category: Large Structures]]
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[[Category: Fujihashi M]]
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==Reference==
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[[Category: Hagihara H]]
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<ref group="xtra">PMID:12719434</ref><references group="xtra"/>
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[[Category: Ito S]]
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[[Category: Alpha-amylase]]
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[[Category: Kita A]]
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[[Category: Bacteria]]
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[[Category: Miki K]]
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[[Category: Fujihashi, M.]]
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[[Category: Nonaka T]]
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[[Category: Hagihara, H.]]
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[[Category: Ozaki K]]
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[[Category: Ito, S.]]
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[[Category: Kita, A.]]
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[[Category: Miki, K.]]
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[[Category: Nonaka, T.]]
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[[Category: Ozaki, K.]]
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[[Category: Alkaline]]
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[[Category: Alpha-amylase]]
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[[Category: Calcium-free]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:51:42 2009''
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Current revision

Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38)

PDB ID 1ud2

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OCA

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