8rzi
From Proteopedia
(Difference between revisions)
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| - | '''Unreleased structure''' | ||
| - | + | ==ZgGH129 from Zobellia galactanivorans soaked with 1,2-diF-ADG (3,6-Anhydro-2-deoxy-2-fluoro-a-D-galactopyranosyl fluoride) resulting in a trapped glycosyl-enzyme intermediate.== | |
| + | <StructureSection load='8rzi' size='340' side='right'caption='[[8rzi]], [[Resolution|resolution]] 1.96Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[8rzi]] 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=8RZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8RZI FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1H37:(1~{R},4~{S},5~{S},8~{S})-4-fluoranyl-2,6-dioxabicyclo[3.2.1]octan-8-ol'>A1H37</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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=8rzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rzi OCA], [https://pdbe.org/8rzi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8rzi RCSB], [https://www.ebi.ac.uk/pdbsum/8rzi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8rzi ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/G0L004_ZOBGA G0L004_ZOBGA] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The marine Bacteroidota Zobellia galactanivorans has a polysaccharide utilization locus dedicated to the catabolism of the red algal cell wall galactan carrageenan and its unique and industrially important alpha-3,6-anhydro-D-galactose (ADG) monosaccharide. Here we present the first analysis of the specific molecular interactions the exo-(alpha-1,3)-3,6-anhydro-D-galactosidase ZgGH129 uses to cope with the strict steric restrictions imposed by its bicyclic ADG substrate - which is ring flipped relative to D-galactose. Crystallographic snapshots of key catalytic states obtained with the natural substrate and novel chemical tools designed to mimic species along the reaction coordinate, together with quantum mechanics/molecular mechanics (QM/MM) metadynamics methods and kinetic studies, demonstrate a retaining mechanism where the second step is rate limiting. The conformational landscape of the constrained 3,6-anhydro-D-galactopyranose ring proceeds through enzyme glycosylation B1,4 --> [E4]double dagger --> E4/1C4 and deglycosylation E4/1C4 --> [E4]double dagger --> B1,4 itineraries limited to the Southern Hemisphere of the Cremer-Pople sphere. These results demonstrate the conformational changes throughout catalysis in a non-standard, sterically restrained, bicyclic monosaccharide and provide a molecular framework for mechanism-based inhibitor design for anhydro-type carbohydrate-processing enzymes and for future applications involving carrageenan degradation. In addition, it provides a rare example of distinct niche-based conformational itineraries within the same carbohydrate-active enzyme family. | ||
| - | + | Constrained Catalytic Itinerary of a Retaining 3,6-Anhydro-D-Galactosidase, a Key Enzyme in Red Algal Cell Wall Degradation.,Wallace MD, Cuxart I, Roret T, Guee L, Debowski AW, Czjzek M, Rovira C, Stubbs KA, Ficko-Blean E Angew Chem Int Ed Engl. 2024 Jul 18:e202411171. doi: 10.1002/anie.202411171. PMID:39022920<ref>PMID:39022920</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 8rzi" style="background-color:#fffaf0;"></div> |
| - | [[Category: Ficko-Blean | + | == References == |
| - | [[Category: | + | <references/> |
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Zobellia galactanivorans]] | ||
| + | [[Category: Czjzek M]] | ||
| + | [[Category: Ficko-Blean E]] | ||
| + | [[Category: Roret T]] | ||
Current revision
ZgGH129 from Zobellia galactanivorans soaked with 1,2-diF-ADG (3,6-Anhydro-2-deoxy-2-fluoro-a-D-galactopyranosyl fluoride) resulting in a trapped glycosyl-enzyme intermediate.
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