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New page: left|200px<br /><applet load="1o4z" size="450" color="white" frame="true" align="right" spinBox="true" caption="1o4z, resolution 2.3Å" /> '''THE THREE-DIMENSIONAL...
 
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[[Image:1o4z.jpg|left|200px]]<br /><applet load="1o4z" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1o4z, resolution 2.3&Aring;" />
'''THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE B FROM ZOBELLIA GALACTANIVORANS'''<br />


==Overview==
==THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE B FROM ZOBELLIA GALACTANIVORANS==
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.
<StructureSection load='1o4z' size='340' side='right'caption='[[1o4z]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1o4z]] is a 4 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=1O4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O4Z FirstGlance]. <br>
1O4Z is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Zobellia_galactanivorans Zobellia galactanivorans] with MG, NA and EPE as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Beta-agarase Beta-agarase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.81 3.2.1.81] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1O4Z OCA].
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1o4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o4z OCA], [https://pdbe.org/1o4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o4z RCSB], [https://www.ebi.ac.uk/pdbsum/1o4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o4z ProSAT]</span></td></tr>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12970344 12970344]
</table>
[[Category: Beta-agarase]]
== Function ==
[[Category: Single protein]]
[https://www.uniprot.org/uniprot/AGAB_ZOBGA AGAB_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. Also tolerant to hybrid substrates containing C6-sulfate groups at the -4, +1, and +3 positions.<ref>PMID:15456406</ref> <ref>PMID:22778272</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o4/1o4z_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1o4z ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Zobellia galactanivorans]]
[[Category: Zobellia galactanivorans]]
[[Category: Allouch, J.]]
[[Category: Allouch J]]
[[Category: Barbeyron, T.]]
[[Category: Barbeyron T]]
[[Category: Czjzek, M.]]
[[Category: Czjzek M]]
[[Category: Helbert, W.]]
[[Category: Helbert W]]
[[Category: Henrissat, B.]]
[[Category: Henrissat B]]
[[Category: Jam, M.]]
[[Category: Jam M]]
[[Category: Kloareg, B.]]
[[Category: Kloareg B]]
[[Category: EPE]]
[[Category: MG]]
[[Category: NA]]
[[Category: 4-d-galactose linkages]]
[[Category: agarose degradation]]
[[Category: beta-agarase]]
[[Category: cleavage of beta-1]]
[[Category: glycoside hydrolase family 16]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:21:07 2007''

Latest revision as of 06:09, 3 April 2024

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

1o4z, resolution 2.30Å

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