1dyp

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(New page: 200px<br /><applet load="1dyp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dyp, resolution 1.54&Aring;" /> '''1,3-ALPHA-1,4-BETA-D...)
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[[Image:1dyp.gif|left|200px]]<br /><applet load="1dyp" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1dyp, resolution 1.54&Aring;" />
caption="1dyp, resolution 1.54&Aring;" />
'''1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE 4 GALACTOHYDROLASE'''<br />
'''1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE 4 GALACTOHYDROLASE'''<br />
==Overview==
==Overview==
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BACKGROUND: kappa-carrageenans are gel-forming, sulfated, 1,3-alpha-1,4-beta-galactans from the cell walls of marine red algae. The, kappa-carrageenase from the marine, gram-negative bacterium, Pseudoalteromonas carrageenovora degrades kappa-carrageenan both in, solution and in solid state by an endoprocessive mechanism. This, beta-galactanase belongs to the clan-B of glycoside hydrolases. RESULTS:, The structure of P. carrageenovora kappa-carrageenase has been solved to, 1.54 A resolution by the multiwavelength anomalous diffraction (MAD), method, using a seleno-methionine-substituted form of the enzyme. The, enzyme folds into a curved beta sandwich, with a tunnel-like active site, cavity. Another remarkable characteristic is the presence of an arginine, residue at subsite -1. CONCLUSIONS: The crystal structure of P., carrageenovora kappa-carrageenase is the first three-dimensional structure, of a carrageenase. Its tunnel-shaped active site, the first to be reported, for enzymes other than cellulases, suggests that such tunnels are, associated with the degradation of solid polysaccharides. Clan-B glycoside, hydrolases fall into two subgroups, one with catalytic machinery held by, an ancestral beta bulge, and the other in which it is held by a regular, beta strand. At subsite -1, all of these hydrolases exhibit an aromatic, amino acid that interacts with the hexopyranose ring of the monosaccharide, undergoing catalysis. In addition, in kappa-carrageenases, an arginine, residue recognizes the sulfate-ester substituents of the beta-linked, kappa-carrageenan monomers. It also appears that, in addition to the, nucleophile and acid/base catalysts, two other amino acids are involved, with the catalytic cycle, accelerating the deglycosylation step.
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BACKGROUND: kappa-carrageenans are gel-forming, sulfated 1,3-alpha-1,4-beta-galactans from the cell walls of marine red algae. The kappa-carrageenase from the marine, gram-negative bacterium Pseudoalteromonas carrageenovora degrades kappa-carrageenan both in solution and in solid state by an endoprocessive mechanism. This beta-galactanase belongs to the clan-B of glycoside hydrolases. RESULTS: The structure of P. carrageenovora kappa-carrageenase has been solved to 1.54 A resolution by the multiwavelength anomalous diffraction (MAD) method, using a seleno-methionine-substituted form of the enzyme. The enzyme folds into a curved beta sandwich, with a tunnel-like active site cavity. Another remarkable characteristic is the presence of an arginine residue at subsite -1. CONCLUSIONS: The crystal structure of P. carrageenovora kappa-carrageenase is the first three-dimensional structure of a carrageenase. Its tunnel-shaped active site, the first to be reported for enzymes other than cellulases, suggests that such tunnels are associated with the degradation of solid polysaccharides. Clan-B glycoside hydrolases fall into two subgroups, one with catalytic machinery held by an ancestral beta bulge, and the other in which it is held by a regular beta strand. At subsite -1, all of these hydrolases exhibit an aromatic amino acid that interacts with the hexopyranose ring of the monosaccharide undergoing catalysis. In addition, in kappa-carrageenases, an arginine residue recognizes the sulfate-ester substituents of the beta-linked kappa-carrageenan monomers. It also appears that, in addition to the nucleophile and acid/base catalysts, two other amino acids are involved with the catalytic cycle, accelerating the deglycosylation step.
==About this Structure==
==About this Structure==
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1DYP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudoalteromonas_carrageenovora Pseudoalteromonas carrageenovora] with CD and CL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Kappa-carrageenase Kappa-carrageenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.83 3.2.1.83] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DYP OCA].
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1DYP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudoalteromonas_carrageenovora Pseudoalteromonas carrageenovora] with <scene name='pdbligand=CD:'>CD</scene> and <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Kappa-carrageenase Kappa-carrageenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.83 3.2.1.83] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DYP OCA].
==Reference==
==Reference==
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[[Category: kappa-carrageenan double helix degradation]]
[[Category: kappa-carrageenan double helix degradation]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:41:14 2007''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:21:57 2008''

Revision as of 10:21, 21 February 2008


1dyp, resolution 1.54Å

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1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE 4 GALACTOHYDROLASE

Overview

BACKGROUND: kappa-carrageenans are gel-forming, sulfated 1,3-alpha-1,4-beta-galactans from the cell walls of marine red algae. The kappa-carrageenase from the marine, gram-negative bacterium Pseudoalteromonas carrageenovora degrades kappa-carrageenan both in solution and in solid state by an endoprocessive mechanism. This beta-galactanase belongs to the clan-B of glycoside hydrolases. RESULTS: The structure of P. carrageenovora kappa-carrageenase has been solved to 1.54 A resolution by the multiwavelength anomalous diffraction (MAD) method, using a seleno-methionine-substituted form of the enzyme. The enzyme folds into a curved beta sandwich, with a tunnel-like active site cavity. Another remarkable characteristic is the presence of an arginine residue at subsite -1. CONCLUSIONS: The crystal structure of P. carrageenovora kappa-carrageenase is the first three-dimensional structure of a carrageenase. Its tunnel-shaped active site, the first to be reported for enzymes other than cellulases, suggests that such tunnels are associated with the degradation of solid polysaccharides. Clan-B glycoside hydrolases fall into two subgroups, one with catalytic machinery held by an ancestral beta bulge, and the other in which it is held by a regular beta strand. At subsite -1, all of these hydrolases exhibit an aromatic amino acid that interacts with the hexopyranose ring of the monosaccharide undergoing catalysis. In addition, in kappa-carrageenases, an arginine residue recognizes the sulfate-ester substituents of the beta-linked kappa-carrageenan monomers. It also appears that, in addition to the nucleophile and acid/base catalysts, two other amino acids are involved with the catalytic cycle, accelerating the deglycosylation step.

About this Structure

1DYP is a Single protein structure of sequence from Pseudoalteromonas carrageenovora with and as ligands. Active as Kappa-carrageenase, with EC number 3.2.1.83 Full crystallographic information is available from OCA.

Reference

The kappa-carrageenase of P. carrageenovora features a tunnel-shaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases., Michel G, Chantalat L, Duee E, Barbeyron T, Henrissat B, Kloareg B, Dideberg O, Structure. 2001 Jun;9(6):513-25. PMID:11435116

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