1ud5: Difference between revisions

Revision as of 11:03, 3 May 2008

Crystal structure of AmyK38 with rubidium ion

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

1UD5 is a Single protein structure of sequence from Bacteria. 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 Sat May 3 11:03:40 2008

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OCA

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 [[Image:1ud5.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1ud5 |SIZE=350|CAPTION= <scene name='initialview01'>1ud5</scene>, resolution 2.70&Aring;
+The line below this paragraph, containing "STRUCTURE_1ud5", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <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>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1ud5|  PDB=1ud5  |  SCENE=  }}
-|RELATEDENTRY=[[1ud2|1UD2]], [[1ud3|1UD3]], [[1ud4|1UD4]], [[1ud6|1UD6]], [[1ud8|1UD8]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ud5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ud5 OCA], [http://www.ebi.ac.uk/pdbsum/1ud5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ud5 RCSB]</span>
-}}
 '''Crystal structure of AmyK38 with rubidium ion'''
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 [[Category: Nonaka, T.]]
 [[Category: Ozaki, K.]]
-[[Category: alkaline]]
+[[Category: Alkaline]]
-[[Category: alpha-amylase]]
+[[Category: Alpha-amylase]]
-[[Category: calcium-free]]
+[[Category: Calcium-free]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 11:03:40 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:08:39 2008''