1bf2
From Proteopedia
(New page: 200px<br /><applet load="1bf2" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bf2, resolution 2.0Å" /> '''STRUCTURE OF PSEUDOMO...) |
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| - | [[Image:1bf2.gif|left|200px]]<br /><applet load="1bf2" size=" | + | [[Image:1bf2.gif|left|200px]]<br /><applet load="1bf2" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1bf2, resolution 2.0Å" /> | caption="1bf2, resolution 2.0Å" /> | ||
'''STRUCTURE OF PSEUDOMONAS ISOAMYLASE'''<br /> | '''STRUCTURE OF PSEUDOMONAS ISOAMYLASE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The three-dimensional structure of isoamylase from Pseudomonas | + | The three-dimensional structure of isoamylase from Pseudomonas amyloderamosa, which hydrolyzes alpha-1,6-glucosidic linkages of amylopectin and glycogen, has been determined by X-ray structure analysis. The enzyme has 750 amino acid residues and a molecular mass of 80 kDa, and it can be crystallized from ammonium sulfate solution. The structure was elucidated by the multiple isomorphous replacement method and refined at 2.2 A resolution, resulting in a final R-factor of 0.161 for significant reflections with a root-mean-square deviation from ideality in bond lengths of 0.009 A. The analysis revealed that in the N-terminal region, isoamylase has a novel extra domain that we call domain N, whose three-dimensional structure has not so far been reported. It has a (beta/alpha)8-barrel-type supersecondary structure in the catalytic domain common to the alpha-amylase family enzymes, though the barrel is incomplete, with a deletion of an alpha-helix between the fifth and sixth beta-strands. A long excursed region is present between the third beta-strand and the third alpha-helix of the barrel but, in contrast to the so-called domain B that has been identified in the other enzymes of alpha-amylase family, it cannot be considered to be an independent domain, because this loop forms a globular cluster together with the loop between the fourth beta-strand and the fourth alpha-helix. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other alpha-amylase family enzymes. |
==About this Structure== | ==About this Structure== | ||
| - | 1BF2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_amyloderamosa Pseudomonas amyloderamosa] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Isoamylase Isoamylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.68 3.2.1.68] Full crystallographic information is available from [http:// | + | 1BF2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_amyloderamosa Pseudomonas amyloderamosa] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Isoamylase Isoamylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.68 3.2.1.68] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BF2 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: hydrolase]] | [[Category: hydrolase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:54:34 2008'' |
Revision as of 09:54, 21 February 2008
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STRUCTURE OF PSEUDOMONAS ISOAMYLASE
Overview
The three-dimensional structure of isoamylase from Pseudomonas amyloderamosa, which hydrolyzes alpha-1,6-glucosidic linkages of amylopectin and glycogen, has been determined by X-ray structure analysis. The enzyme has 750 amino acid residues and a molecular mass of 80 kDa, and it can be crystallized from ammonium sulfate solution. The structure was elucidated by the multiple isomorphous replacement method and refined at 2.2 A resolution, resulting in a final R-factor of 0.161 for significant reflections with a root-mean-square deviation from ideality in bond lengths of 0.009 A. The analysis revealed that in the N-terminal region, isoamylase has a novel extra domain that we call domain N, whose three-dimensional structure has not so far been reported. It has a (beta/alpha)8-barrel-type supersecondary structure in the catalytic domain common to the alpha-amylase family enzymes, though the barrel is incomplete, with a deletion of an alpha-helix between the fifth and sixth beta-strands. A long excursed region is present between the third beta-strand and the third alpha-helix of the barrel but, in contrast to the so-called domain B that has been identified in the other enzymes of alpha-amylase family, it cannot be considered to be an independent domain, because this loop forms a globular cluster together with the loop between the fourth beta-strand and the fourth alpha-helix. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other alpha-amylase family enzymes.
About this Structure
1BF2 is a Single protein structure of sequence from Pseudomonas amyloderamosa with as ligand. Active as Isoamylase, with EC number 3.2.1.68 Full crystallographic information is available from OCA.
Reference
Three-dimensional structure of Pseudomonas isoamylase at 2.2 A resolution., Katsuya Y, Mezaki Y, Kubota M, Matsuura Y, J Mol Biol. 1998 Sep 4;281(5):885-97. PMID:9719642
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