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| | <StructureSection load='1o4z' size='340' side='right'caption='[[1o4z]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='1o4z' size='340' side='right'caption='[[1o4z]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1o4z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"cytophaga_drobachiensis"_barbeyron_et_al._1998 "cytophaga drobachiensis" barbeyron et al. 1998]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1O4Z FirstGlance]. <br> | + | <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> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">agaB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63186 "Cytophaga drobachiensis" Barbeyron et al. 1998])</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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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=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> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1o4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o4z OCA], [http://pdbe.org/1o4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1o4z RCSB], [http://www.ebi.ac.uk/pdbsum/1o4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1o4z ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cytophaga drobachiensis barbeyron et al. 1998]] | |
| - | [[Category: Beta-agarase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Allouch, J]] | + | [[Category: Zobellia galactanivorans]] |
| - | [[Category: Barbeyron, T]] | + | [[Category: Allouch J]] |
| - | [[Category: Czjzek, M]] | + | [[Category: Barbeyron T]] |
| - | [[Category: Helbert, W]] | + | [[Category: Czjzek M]] |
| - | [[Category: Henrissat, B]] | + | [[Category: Helbert W]] |
| - | [[Category: Jam, M]] | + | [[Category: Henrissat B]] |
| - | [[Category: Kloareg, B]] | + | [[Category: Jam M]] |
| - | [[Category: 4-d-galactose linkage]]
| + | [[Category: Kloareg B]] |
| - | [[Category: Agarose degradation]]
| + | |
| - | [[Category: Cleavage of beta-1]]
| + | |
| - | [[Category: Glycoside hydrolase family 16]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
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.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Jam M, Flament D, Allouch J, Potin P, Thion L, Kloareg B, Czjzek M, Helbert W, Michel G, Barbeyron T. The endo-beta-agarases AgaA and AgaB from the marine bacterium Zobellia galactanivorans: two paralogue enzymes with different molecular organizations and catalytic behaviours. Biochem J. 2005 Feb 1;385(Pt 3):703-13. PMID:15456406 doi:http://dx.doi.org/10.1042/BJ20041044
- ↑ Hehemann JH, Correc G, Thomas F, Bernard T, Barbeyron T, Jam M, Helbert W, Michel G, Czjzek M. Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans. J Biol Chem. 2012 Jul 9. PMID:22778272 doi:10.1074/jbc.M112.377184
- ↑ Allouch J, Jam M, Helbert W, Barbeyron T, Kloareg B, Henrissat B, Czjzek M. The three-dimensional structures of two beta-agarases. J Biol Chem. 2003 Nov 21;278(47):47171-80. Epub 2003 Sep 11. PMID:12970344 doi:http://dx.doi.org/10.1074/jbc.M308313200
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