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| | <StructureSection load='4bq4' size='340' side='right'caption='[[4bq4]], [[Resolution|resolution]] 2.05Å' scene=''> | | <StructureSection load='4bq4' size='340' side='right'caption='[[4bq4]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4bq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Microbulbifer_degradans_2-40 Microbulbifer degradans 2-40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BQ4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4bq4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BQ4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AAL:3,6-ANHYDRO-L-GALACTOSE'>AAL</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | + | </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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=AAL:3,6-ANHYDRO-L-GALACTOSE'>AAL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4bq2|4bq2]], [[4bq3|4bq3]], [[4bq5|4bq5]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4bq2|4bq2]], [[4bq3|4bq3]], [[4bq5|4bq5]]</div></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='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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bq4 OCA], [http://pdbe.org/4bq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bq4 RCSB], [http://www.ebi.ac.uk/pdbsum/4bq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bq4 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=4bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bq4 OCA], [https://pdbe.org/4bq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bq4 RCSB], [https://www.ebi.ac.uk/pdbsum/4bq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bq4 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | [[Category: Beta-agarase]] | | [[Category: Beta-agarase]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Microbulbifer degradans 2-40]] | |
| | [[Category: Boraston, A B]] | | [[Category: Boraston, A B]] |
| | [[Category: Hehemann, J H]] | | [[Category: Hehemann, J H]] |
| | [[Category: Pluvinage, B]] | | [[Category: Pluvinage, B]] |
| | [[Category: Hydrolase]] | | [[Category: Hydrolase]] |
| Structural highlights
Publication Abstract from PubMed
The bacteria that metabolize agarose use multiple enzymes of complementary specificities to hydrolyze the glycosidic linkages in agarose, a linear polymer comprising the repeating disaccharide subunit of neoagarobiose (3,6-anhydro-L-galactose-alpha-(1,3)-D-galactose), which are beta-(1,4)-linked. Here we present the crystal structure of a glycoside hydrolase family 50 exo-beta-agarase Aga50D from the marine microbe Saccharophagus degradans. This enzyme catalyzes a critical step in the metabolism of agarose by S. degradans through cleaving agarose oligomers into neoagarobiose products that can be further processed into monomers. The crystal structure of Aga50D to 1.9 &{Aring] resolution reveals a (beta/alpha)8-barrel fold that is elaborated with a beta-sandwich domain and extensive loops. The structure of catalytically inactivated Aga50D in complex with non-hydrolyzed neoagarotetraose (2.05 &{Aring] resolution) and neoagarooctaose (2.30 &{Aring] resolution) provide views of Michaelis complexes for a beta-agarase. In these structures, the D-galactose residue in the -1 subsite is distorted into a 1S3 skew boat conformation. The relative positioning of the putative catalytic residues are most consistent with a retaining catalytic mechanism. Additionally, the neoagarooctaose complex showed that this extended substrate made substantial interactions with the beta-sandwich domain, which resembles a carbohydrate binding module, thus creating additional plus (+) subsites and funneling the polymeric substrate through the tunnel shaped active site. A synthesis of these results in combination with an additional neoagarobiose product complex suggests a potential exo-processive mode of action of Aga50D on the agarose double helix.
Substrate recognition and hydrolysis by a family 50 exo-beta-agarase Aga50D from the marine bacterium Saccharophagus degradans.,Pluvinage B, Hehemann JH, Boraston AB J Biol Chem. 2013 Aug 6. PMID:23921382[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Pluvinage B, Hehemann JH, Boraston AB. Substrate recognition and hydrolysis by a family 50 exo-beta-agarase Aga50D from the marine bacterium Saccharophagus degradans. J Biol Chem. 2013 Aug 6. PMID:23921382 doi:10.1074/jbc.M113.491068
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