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1dyp
From Proteopedia
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|PDB= 1dyp |SIZE=350|CAPTION= <scene name='initialview01'>1dyp</scene>, resolution 1.54Å | |PDB= 1dyp |SIZE=350|CAPTION= <scene name='initialview01'>1dyp</scene>, resolution 1.54Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene> | + | |LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= CGKA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227 Pseudoalteromonas carrageenovora]) | |GENE= CGKA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227 Pseudoalteromonas carrageenovora]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dyp OCA], [http://www.ebi.ac.uk/pdbsum/1dyp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dyp RCSB]</span> | ||
}} | }} | ||
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[[Category: Dideberg, O.]] | [[Category: Dideberg, O.]] | ||
[[Category: Michel, G.]] | [[Category: Michel, G.]] | ||
| - | [[Category: CD]] | ||
| - | [[Category: CL]] | ||
[[Category: hydrolase]] | [[Category: hydrolase]] | ||
[[Category: kappa-carrageenan double helix degradation]] | [[Category: kappa-carrageenan double helix degradation]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:51:27 2008'' |
Revision as of 16:51, 30 March 2008
| |||||||
| , resolution 1.54Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | CGKA (Pseudoalteromonas carrageenovora) | ||||||
| Activity: | Kappa-carrageenase, with EC number 3.2.1.83 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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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