1dyp
From Proteopedia
(Difference between revisions)
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<StructureSection load='1dyp' size='340' side='right'caption='[[1dyp]], [[Resolution|resolution]] 1.54Å' scene=''> | <StructureSection load='1dyp' size='340' side='right'caption='[[1dyp]], [[Resolution|resolution]] 1.54Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
- | <table><tr><td colspan='2'>[[1dyp]] is a 1 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[1dyp]] is a 1 chain structure with sequence from [https://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]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DYP FirstGlance]. <br> |
- | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.54Å</td></tr> |
- | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
- | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dyp OCA], [https://pdbe.org/1dyp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dyp RCSB], [https://www.ebi.ac.uk/pdbsum/1dyp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dyp ProSAT]</span></td></tr> | |
- | + | ||
- | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
+ | == Function == | ||
+ | [https://www.uniprot.org/uniprot/CGKA_PSEVC CGKA_PSEVC] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dyp ConSurf]. | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dyp ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
- | <div style="background-color:#fffaf0;"> | ||
- | == Publication Abstract from PubMed == | ||
- | 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. | ||
- | |||
- | 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<ref>PMID:11435116</ref> | ||
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- | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
- | </div> | ||
- | <div class="pdbe-citations 1dyp" style="background-color:#fffaf0;"></div> | ||
- | == References == | ||
- | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
- | [[Category: Atcc 43555]] | ||
- | [[Category: Kappa-carrageenase]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
- | [[Category: | + | [[Category: Pseudoalteromonas carrageenovora]] |
- | [[Category: | + | [[Category: Chantalat L]] |
- | [[Category: | + | [[Category: Dideberg O]] |
- | [[Category: | + | [[Category: Michel G]] |
- | + |
Revision as of 09:55, 20 March 2024
1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE 4 GALACTOHYDROLASE
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