1ud8: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1ud8]] is a 1 chain structure with sequence from [http://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=1UD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UD8 FirstGlance]. <br> | <table><tr><td colspan='2'>[[1ud8]] is a 1 chain structure with sequence from [http://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=1UD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UD8 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>< | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ud2|1ud2]], [[1ud3|1ud3]], [[1ud4|1ud4]], [[1ud5|1ud5]], [[1ud6|1ud6]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ud2|1ud2]], [[1ud3|1ud3]], [[1ud4|1ud4]], [[1ud5|1ud5]], [[1ud6|1ud6]]</td></tr> | ||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ud8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ud8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ud8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ud8 PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ud8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ud8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ud8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ud8 PDBsum]</span></td></tr> | ||
<table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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==See Also== | ==See Also== | ||
*[[Amylase|Amylase]] | *[[Amylase|Amylase]] | ||
*[[User:Gabriel Pons/Sandbox 2|User:Gabriel Pons/Sandbox 2]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Alpha-amylase]] | [[Category: Alpha-amylase]] | ||
[[Category: Bacillus sp. ksm-k38]] | [[Category: Bacillus sp. ksm-k38]] | ||
[[Category: Fujihashi, M | [[Category: Fujihashi, M]] | ||
[[Category: Hagihara, H | [[Category: Hagihara, H]] | ||
[[Category: Ito, S | [[Category: Ito, S]] | ||
[[Category: Kita, A | [[Category: Kita, A]] | ||
[[Category: Miki, K | [[Category: Miki, K]] | ||
[[Category: Nonaka, T | [[Category: Nonaka, T]] | ||
[[Category: Ozaki, K | [[Category: Ozaki, K]] | ||
[[Category: Alkaline]] | [[Category: Alkaline]] | ||
[[Category: Calcium-free]] | [[Category: Calcium-free]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
Revision as of 15:55, 6 January 2015
Crystal structure of AmyK38 with lithium ionCrystal structure of AmyK38 with lithium ion
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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