1dyp
From Proteopedia
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- | [[Image:1dyp.gif|left|200px]] | + | [[Image:1dyp.gif|left|200px]] |
- | + | ||
- | '''1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE 4 GALACTOHYDROLASE''' | + | {{Structure |
+ | |PDB= 1dyp |SIZE=350|CAPTION= <scene name='initialview01'>1dyp</scene>, resolution 1.54Å | ||
+ | |SITE= | ||
+ | |LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene> and <scene name='pdbligand=CL:CHLORIDE ION'>CL</scene> | ||
+ | |ACTIVITY= [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] | ||
+ | |GENE= CGKA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227 Pseudoalteromonas carrageenovora]) | ||
+ | }} | ||
+ | |||
+ | '''1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE 4 GALACTOHYDROLASE''' | ||
+ | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
- | 1DYP is a [ | + | 1DYP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudoalteromonas_carrageenovora Pseudoalteromonas carrageenovora]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DYP OCA]. |
==Reference== | ==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:[http:// | + | 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:[http://www.ncbi.nlm.nih.gov/pubmed/11435116 11435116] |
[[Category: Kappa-carrageenase]] | [[Category: Kappa-carrageenase]] | ||
[[Category: Pseudoalteromonas carrageenovora]] | [[Category: Pseudoalteromonas carrageenovora]] | ||
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[[Category: kappa-carrageenan double helix degradation]] | [[Category: kappa-carrageenan double helix degradation]] | ||
- | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:46:40 2008'' |
Revision as of 08:46, 20 March 2008
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, resolution 1.54Å | |||||||
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Ligands: | and | ||||||
Gene: | CGKA (Pseudoalteromonas carrageenovora) | ||||||
Activity: | Kappa-carrageenase, with EC number 3.2.1.83 | ||||||
Coordinates: | save as pdb, mmCIF, xml |
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. 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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