2die
From Proteopedia
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|PDB= 2die |SIZE=350|CAPTION= <scene name='initialview01'>2die</scene>, resolution 2.1Å | |PDB= 2die |SIZE=350|CAPTION= <scene name='initialview01'>2die</scene>, resolution 2.1Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2die FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2die OCA], [http://www.ebi.ac.uk/pdbsum/2die PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2die RCSB]</span> | ||
}} | }} | ||
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[[Category: Ozawa, T.]] | [[Category: Ozawa, T.]] | ||
[[Category: Shirai, T.]] | [[Category: Shirai, T.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: NA]] | ||
[[Category: beta-alpha-barrel]] | [[Category: beta-alpha-barrel]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:34:59 2008'' |
Revision as of 23:35, 30 March 2008
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| , resolution 2.1Å | |||||||
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| Ligands: | , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Alkaline alpha-amylase AmyK from Bacillus sp. KSM-1378
Overview
The crystal structure of alkaline liquefying alpha-amylase (AmyK) from the alkaliphilic Bacillus sp. KSM-1378 was determined at 2.1 A resolution. The AmyK structure belongs to the GH13 glycoside hydrolase family, which consists of three domains, and bound three calcium and one sodium ions. The alkaline adaptation mechanism of AmyK was investigated by the ancestral sequence evolutionary trace method and by extensive comparisons between alkaline and nonalkaline enzyme structures, including three other protein families: protease, cellulase, and phosphoserine aminotransferase. The consensus change for the alkaline adaptation process was a decrease in the Lys content. The loss of a Lys residue is associated with ion pair remodeling, which mainly consists of the loss of Lys-Asp/Glu ion pairs and the acquisition of Arg ion pairs, preferably Arg-Glu. The predicted replacements of the positively charged amino acids were often, although not always, used for ion pair remodeling.
About this Structure
2DIE is a Single protein structure of sequence from Bacillus sp.. Full crystallographic information is available from OCA.
Reference
Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins., Shirai T, Igarashi K, Ozawa T, Hagihara H, Kobayashi T, Ozaki K, Ito S, Proteins. 2007 Feb 15;66(3):600-10. PMID:17154418
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