1ud3: Difference between revisions

Revision as of 16:23, 21 February 2008

Crystal structure of AmyK38 N289H mutant

OverviewOverview

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 StructureAbout this Structure

1UD3 is a Single protein structure of sequence from Bacillus sp. ksm-k38 with as ligand. Active as Alpha-amylase, with EC number 3.2.1.1 Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Feb 21 15:23:17 2008

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-[[Image:1ud3.jpg|left|200px]]<br /><applet load="1ud3" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1ud3.jpg|left|200px]]<br /><applet load="1ud3" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1ud3, resolution 2.15&Aring;" />
 '''Crystal structure of AmyK38 N289H mutant'''<br />
 ==Overview==
-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.
+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==
-UD3 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 as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1UD3 OCA].
+UD3 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 <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1UD3 OCA].
 ==Reference==
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 [[Category: calcium-free]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:46:38 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:23:17 2008''