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| | <StructureSection load='4asm' size='340' side='right'caption='[[4asm]], [[Resolution|resolution]] 1.50Å' scene=''> | | <StructureSection load='4asm' size='340' side='right'caption='[[4asm]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4asm]] is a 1 chain structure with sequence from [https://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=4ASM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ASM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4asm]] 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=4ASM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ASM FirstGlance]. <br> |
| - | </td></tr><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=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.5Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-agarase Beta-agarase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.81 3.2.1.81] </span></td></tr>
| + | <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=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=4asm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4asm OCA], [https://pdbe.org/4asm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4asm RCSB], [https://www.ebi.ac.uk/pdbsum/4asm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4asm ProSAT]</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=4asm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4asm OCA], [https://pdbe.org/4asm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4asm RCSB], [https://www.ebi.ac.uk/pdbsum/4asm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4asm ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/AGAD_ZOBGA AGAD_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. Requires at least 4 consecutive agarose units and is highly intolerant to modifications.<ref>PMID:22778272</ref>
| + | [https://www.uniprot.org/uniprot/AGAD_ZOBGA AGAD_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. Requires at least 4 consecutive agarose units and is highly intolerant to modifications.<ref>PMID:22778272</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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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: Bernard, T]] | + | [[Category: Zobellia galactanivorans]] |
| - | [[Category: Correc, G]] | + | [[Category: Bernard T]] |
| - | [[Category: Czjzek, M]] | + | [[Category: Correc G]] |
| - | [[Category: Hehemann, J H]] | + | [[Category: Czjzek M]] |
| - | [[Category: Michel, G]] | + | [[Category: Hehemann JH]] |
| - | [[Category: Endo-beta-agarase]]
| + | [[Category: Michel G]] |
| - | [[Category: Glycoside hydrolase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
AGAD_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. Requires at least 4 consecutive agarose units and is highly intolerant to modifications.[1]
Publication Abstract from PubMed
Zobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. Notably this marine Bacteroidetes possesses a complex agarolytic system comprising 4 beta-agarases and 5 beta-porphyranases, all belonging to the glycoside hydrolase family 16. While beta-agarases are specific for the neutral agarobiose motives, the recently discovered beta-porphyranases degrade the sulfated polymers found in various quantities in natural agars. Here we report the biochemical and structural comparison of five beta-porphyranases and beta-agarases from Z. galactanivorans. The respective degradation patterns of two beta-porphyranases and three beta-agarases are analyzed by their action on defined hybrid oligosaccharides. In the light of the high resolution crystal structures the biochemical results allow a detailed mapping of substrate specificities along the enzymes active site groove. While PorA displays a strict requirement for C6-sulfate in the -2 and +1 binding subsites, PorB tolerates the presence of 3-6-anhydro-L-galactose in subsite -2. Both enzymes do not accept methylation of the galactose unit in the -1 subsite. The beta-agarase AgaD requires at least five consecutive agarose units (DP10) and is highly intolerant to modifications, whereas for AgaB oligosaccharides containing C6-sulfate groups at the -4, +1 and +3 positions are still degraded. Together with a transcriptional analysis of the expression of these enzymes, the structural and biochemical results allow proposition of a model scheme for the agarolytic system of Z. galactanivorans.
Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans.,Hehemann JH, Correc G, Thomas F, Bernard T, Barbeyron T, Jam M, Helbert W, Michel G, Czjzek M J Biol Chem. 2012 Jul 9. PMID:22778272[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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
- ↑ 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
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