1o4y

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{{Seed}}
 
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[[Image:1o4y.png|left|200px]]
 
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==THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE A FROM ZOBELLIA GALACTANIVORANS==
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The line below this paragraph, containing "STRUCTURE_1o4y", creates the "Structure Box" on the page.
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<StructureSection load='1o4y' size='340' side='right'caption='[[1o4y]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1o4y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zobellia_galactanivorans Zobellia galactanivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O4Y FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.48&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_1o4y| PDB=1o4y | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1o4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o4y OCA], [https://pdbe.org/1o4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o4y RCSB], [https://www.ebi.ac.uk/pdbsum/1o4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o4y ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/AGAA_ZOBGA AGAA_ZOBGA] Cleaves the beta-1,4-linkages between beta-D-galactose and alpha-L-3,6-anhydro-galactose residues in agarose. Cleaves agarose in a random manner with retention of the anomeric-bond configuration, producing beta-anomers that give rise progressively to alpha-anomers when mutarotation takes place.<ref>PMID:15456406</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o4/1o4y_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1o4y ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two beta-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 A for beta-agarases A and B, respectively. The structure of beta-agarase A was solved by the multiple anomalous diffraction method, whereas beta-agarase B was solved with molecular replacement using beta-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the beta-agarases.
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===THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE A FROM ZOBELLIA GALACTANIVORANS===
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The three-dimensional structures of two beta-agarases.,Allouch J, Jam M, Helbert W, Barbeyron T, Kloareg B, Henrissat B, Czjzek M J Biol Chem. 2003 Nov 21;278(47):47171-80. Epub 2003 Sep 11. PMID:12970344<ref>PMID:12970344</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_12970344}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1o4y" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 12970344 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12970344}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1O4Y is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Zobellia_galactanivorans Zobellia galactanivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O4Y OCA].
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==Reference==
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The three-dimensional structures of two beta-agarases., Allouch J, Jam M, Helbert W, Barbeyron T, Kloareg B, Henrissat B, Czjzek M, J Biol Chem. 2003 Nov 21;278(47):47171-80. Epub 2003 Sep 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12970344 12970344]
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[[Category: Beta-agarase]]
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[[Category: Single protein]]
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[[Category: Zobellia galactanivorans]]
[[Category: Zobellia galactanivorans]]
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[[Category: Allouch, J.]]
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[[Category: Allouch J]]
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[[Category: Barbeyron, T.]]
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[[Category: Barbeyron T]]
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[[Category: Czjzek, M.]]
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[[Category: Czjzek M]]
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[[Category: Helbert, W.]]
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[[Category: Helbert W]]
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[[Category: Henrissat, B.]]
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[[Category: Henrissat B]]
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[[Category: Jam, M.]]
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[[Category: Jam M]]
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[[Category: Kloareg, B.]]
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[[Category: Kloareg B]]
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[[Category: 4-d-galactose linkage]]
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[[Category: Agarose degradation]]
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[[Category: Beta-agarase]]
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[[Category: Cleavage of beta-1]]
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[[Category: Glycoside hydrolase family 16]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:14:57 2008''
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Current revision

THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE A FROM ZOBELLIA GALACTANIVORANS

PDB ID 1o4y

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