6gl2: Difference between revisions
New page: '''Unreleased structure''' The entry 6gl2 is ON HOLD Authors: Dorival, J., Ruppert, S., Gunnoo, M., Orlowski, A., Chapelais, M., Dabin, J., Labourel, A., Thompson, D., Michel, G., Czjze... |
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The | ==Structure of ZgEngAGH5_4 wild type at 1.2 Angstrom resolution== | ||
<StructureSection load='6gl2' size='340' side='right' caption='[[6gl2]], [[Resolution|resolution]] 1.96Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6gl2]] is a 1 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=6GL2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GL2 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">engA, zobellia_208 ([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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulase Cellulase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.4 3.2.1.4] </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=6gl2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gl2 OCA], [http://pdbe.org/6gl2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gl2 RCSB], [http://www.ebi.ac.uk/pdbsum/6gl2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gl2 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Cell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae-bacteria interactions. The degradation of typical algal polysaccharides, such as agars or alginate, has been intensively studied in this bacterium, but the catabolism of plant-like polysaccharides is essentially uncharacterized. Here we identify a polysaccharide utilization locus in the genome of Z. galactanivorans, induced by laminarin (beta-1,3-glucans), and containing a putative GH5 subfamily 4 (GH5_4) enzyme, currently annotated as a endoglucanase ( Zg EngAGH5_4). A phylogenetic analysis indicates that Zg EngAGH5_4 was laterally acquired from an ancestral Actinobacteria We performed the biochemical and structural characterization of Zg EngAGH5_4 and demonstrate that this GH5 is an endo-beta-glucanase, most active on mixed-linked glucan (MLG). Although Zg EngAGH5_4 and GH16 lichenases both hydrolyze MLG, these two types of enzymes release different series of oligosaccharides. Structural analyses of Zg EngAGH5_4 reveal that all the amino acid residues involved in the catalytic triad and in the negative glucose binding subsites are conserved, when compared to the closest relative, the cellulase EngD from Clostridium cellulovorans, and some other GH5s. In contrast, the positive glucose binding subsites of Zg EngAGH5_4 are different and this could explain the preference for MLG, with respect to cellulose or laminarin. Molecular dynamics computer simulations using different hexaoses reveal that the specificity for MLG occurs through the +1 and +2 subsites of the binding pocket that display the most important differences when compared to the structures of other GH5_4 enzymes. | |||
The laterally-acquired GH5 ZgEngAGH5_4 from the marine bacterium Zobellia galactanivorans is dedicated to hemicellulose hydrolysis.,Dorival J, Ruppert S, Gunnoo M, Orlowski A, Chapelais-Baron M, Dabin J, Labourel A, Thompson D, Michel G, Czjzek M, Genicot S Biochem J. 2018 Oct 19. pii: BCJ20180486. doi: 10.1042/BCJ20180486. PMID:30341165<ref>PMID:30341165</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6gl2" style="background-color:#fffaf0;"></div> | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Cytophaga drobachiensis barbeyron et al. 1998]] | |||
[[Category: Cellulase]] | |||
[[Category: Chapelais, M]] | |||
[[Category: Czjzek, M]] | |||
[[Category: Dabin, J]] | [[Category: Dabin, J]] | ||
[[Category: Dorival, J]] | [[Category: Dorival, J]] | ||
[[Category: Genicot, S]] | [[Category: Genicot, S]] | ||
[[Category: Gunnoo, M]] | [[Category: Gunnoo, M]] | ||
[[Category: Labourel, A]] | [[Category: Labourel, A]] | ||
[[Category: Michel, G]] | |||
[[Category: Orlowski, A]] | [[Category: Orlowski, A]] | ||
[[Category: Ruppert, S]] | |||
[[Category: Thompson, D]] | |||
[[Category: Gh5]] | |||
[[Category: Glycoside hydrolase]] | |||
[[Category: Hydrolase]] | |||
[[Category: Mixed linked glucan]] | |||
[[Category: Zobellia galactanivoran]] | |||
Latest revision as of 10:17, 12 December 2018
Structure of ZgEngAGH5_4 wild type at 1.2 Angstrom resolutionStructure of ZgEngAGH5_4 wild type at 1.2 Angstrom resolution
Structural highlights
Publication Abstract from PubMedCell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae-bacteria interactions. The degradation of typical algal polysaccharides, such as agars or alginate, has been intensively studied in this bacterium, but the catabolism of plant-like polysaccharides is essentially uncharacterized. Here we identify a polysaccharide utilization locus in the genome of Z. galactanivorans, induced by laminarin (beta-1,3-glucans), and containing a putative GH5 subfamily 4 (GH5_4) enzyme, currently annotated as a endoglucanase ( Zg EngAGH5_4). A phylogenetic analysis indicates that Zg EngAGH5_4 was laterally acquired from an ancestral Actinobacteria We performed the biochemical and structural characterization of Zg EngAGH5_4 and demonstrate that this GH5 is an endo-beta-glucanase, most active on mixed-linked glucan (MLG). Although Zg EngAGH5_4 and GH16 lichenases both hydrolyze MLG, these two types of enzymes release different series of oligosaccharides. Structural analyses of Zg EngAGH5_4 reveal that all the amino acid residues involved in the catalytic triad and in the negative glucose binding subsites are conserved, when compared to the closest relative, the cellulase EngD from Clostridium cellulovorans, and some other GH5s. In contrast, the positive glucose binding subsites of Zg EngAGH5_4 are different and this could explain the preference for MLG, with respect to cellulose or laminarin. Molecular dynamics computer simulations using different hexaoses reveal that the specificity for MLG occurs through the +1 and +2 subsites of the binding pocket that display the most important differences when compared to the structures of other GH5_4 enzymes. The laterally-acquired GH5 ZgEngAGH5_4 from the marine bacterium Zobellia galactanivorans is dedicated to hemicellulose hydrolysis.,Dorival J, Ruppert S, Gunnoo M, Orlowski A, Chapelais-Baron M, Dabin J, Labourel A, Thompson D, Michel G, Czjzek M, Genicot S Biochem J. 2018 Oct 19. pii: BCJ20180486. doi: 10.1042/BCJ20180486. PMID:30341165[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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