7dif: Difference between revisions

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<StructureSection load='7dif' size='340' side='right'caption='[[7dif]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
<StructureSection load='7dif' size='340' side='right'caption='[[7dif]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7dif]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum_subsp._longum_JCM_1217 Bifidobacterium longum subsp. longum JCM 1217]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DIF FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DIF 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]] 1.75&#8491;</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]] 1.75&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE0:(1S,2S,3R,4R)-3-(hydroxymethyl)cyclopentane-1,2,4-triol'>FE0</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE0:(1S,2S,3R,4R)-3-(hydroxymethyl)cyclopentane-1,2,4-triol'>FE0</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7dif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dif OCA], [https://pdbe.org/7dif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dif RCSB], [https://www.ebi.ac.uk/pdbsum/7dif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dif 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=7dif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dif OCA], [https://pdbe.org/7dif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dif RCSB], [https://www.ebi.ac.uk/pdbsum/7dif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dif ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HYBA1_BIFL2 HYBA1_BIFL2] Beta-L-arabinofuranosidase that removes the beta-L-arabinofuranose residue from the non-reducing end of various substrates, including beta-L-arabinofuranosyl-hydroxyproline (Ara-Hyp), Ara-beta-1,2-Ara-beta-Hyp (Ara(2)-Hyp), Ara-beta-1,2-Ara-beta-1,2-Ara-beta-Hyp (Ara(3)-Hyp), and beta-L-arabinofuranosyl-(1->2)-1-O-methyl-beta-L-arabinofuranose. In the presence of 1-alkanols, shows transglycosylation activity, retaining the anomeric configuration of the arabinofuranose residue.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The recent discovery of zinc-dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys)(3) (Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on a Zn-coordinated cysteine nucleophile and passing through a thioglycosyl enzyme intermediate, remains controversial. This is primarily due to the expected stability of the intermediate C-S bond. To facilitate the study of this atypical mechanism, we report the synthesis of a cyclophellitol-derived beta-l-arabinofuranosidase inhibitor, hypothesised to react with the catalytic nucleophile to form a non-hydrolysable adduct analogous to the mechanistic covalent intermediate. This beta-l-arabinofuranosidase inhibitor reacts exclusively with the proposed cysteine thiol catalytic nucleophiles of representatives of GH families 127 and 146. X-ray crystal structures determined for the resulting adducts enable MD and QM/MM simulations, which provide insight into the mechanism of thioglycosyl enzyme intermediate breakdown. Leveraging the unique chemistry of cyclophellitol derivatives, the structures and simulations presented here support the assignment of a zinc-coordinated cysteine as the catalytic nucleophile and illuminate the finely tuned energetics of this remarkable metalloenzyme clan.
Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.,McGregor NGS, Coines J, Borlandelli V, Amaki S, Artola M, Nin-Hill A, Linzel D, Yamada C, Arakawa T, Ishiwata A, Ito Y, van der Marel GA, Codee JDC, Fushinobu S, Overkleeft HS, Rovira C, Davies GJ Angew Chem Int Ed Engl. 2021 Mar 8;60(11):5754-5758. doi: 10.1002/anie.202013920. , Epub 2021 Feb 2. PMID:33528085<ref>PMID:33528085</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7dif" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bifidobacterium longum subsp. longum JCM 1217]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Amaki S]]
[[Category: Amaki S]]

Latest revision as of 13:57, 23 October 2024

GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol at 1.75-angstrom resolutionGH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol at 1.75-angstrom resolution

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.75Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

7dif, resolution 1.75Å

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OCA
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