8rzi: Difference between revisions

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New page: '''Unreleased structure''' The entry 8rzi is ON HOLD Authors: Roret, T., Czjzek, M., Ficko-Blean, E. Description: ZgGH129 from Zobellia galactanivorans soaked with 1,2-diF-ADG (3,6-Anh...
 
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'''Unreleased structure'''


The entry 8rzi is ON HOLD
==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]] 1.96&Aring;' 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]] 1.96&#8491;</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 --&gt; [E4]double dagger --&gt; E4/1C4 and deglycosylation E4/1C4 --&gt; [E4]double dagger --&gt; 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.


Authors: Roret, T., Czjzek, M., Ficko-Blean, E.
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>


Description: 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.
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Ficko-Blean, E]]
<div class="pdbe-citations 8rzi" style="background-color:#fffaf0;"></div>
[[Category: Roret, T]]
== References ==
[[Category: Czjzek, M]]
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Zobellia galactanivorans]]
[[Category: Czjzek M]]
[[Category: Ficko-Blean E]]
[[Category: Roret T]]
Retrieved from "https://proteopedia.org/8rzi"