1ud2: Difference between revisions

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-[[Image:1ud2.jpg|left|200px]]<br /><applet load="1ud2" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ud2, resolution 2.13&Aring;" />
-'''Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38)'''<br />
-==Overview==
+==Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38)==
-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.
+<StructureSection load='1ud2' size='340' side='right'caption='[[1ud2]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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>
+<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>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q93I48_9BACI Q93I48_9BACI]
+== 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/ud/1ud2_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=1ud2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-==About this Structure==
+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>
-UD2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp._ksm-k38 Bacillus sp. ksm-k38] with NA and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UD2 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12719434 12719434]
+</div>
-[[Category: Alpha-amylase]]
+<div class="pdbe-citations 1ud2" style="background-color:#fffaf0;"></div>
-[[Category: Bacillus sp. ksm-k38]]
-[[Category: Single protein]]
-[[Category: Fujihashi, M.]]
-[[Category: Hagihara, H.]]
-[[Category: Ito, S.]]
-[[Category: Kita, A.]]
-[[Category: Miki, K.]]
-[[Category: Nonaka, T.]]
-[[Category: Ozaki, K.]]
-[[Category: GOL]]
-[[Category: NA]]
-[[Category: alkaline]]
-[[Category: alpha-amylase]]
-[[Category: calcium-free]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:46:17 2007''
+==See Also==
+*[[Amylase 3D structures|Amylase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bacillus sp. KSM-K38]]
+[[Category: Large Structures]]
+[[Category: Fujihashi M]]
+[[Category: Hagihara H]]
+[[Category: Ito S]]
+[[Category: Kita A]]
+[[Category: Miki K]]
+[[Category: Nonaka T]]
+[[Category: Ozaki K]]