6jeb: Difference between revisions
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<StructureSection load='6jeb' size='340' side='right'caption='[[6jeb]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='6jeb' size='340' side='right'caption='[[6jeb]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6jeb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JEB OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6jeb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Akkermansia_muciniphila_ATCC_BAA-835 Akkermansia muciniphila ATCC BAA-835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JEB FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.498Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACM:ACETAMIDE'>ACM</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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6jeb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jeb OCA], [https://pdbe.org/6jeb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jeb RCSB], [https://www.ebi.ac.uk/pdbsum/6jeb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jeb ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/H2018_AKKM8 H2018_AKKM8] Hydrolyzes terminal GlcNAc residues from terminally unbranched N-glycans and from chitobiose. Hydrolyzes beta-1,6-linked N-acetylglucosamine and beta-1,4-linked N-acetylgalactosamine from pNP-alpha-GalNAc[beta1,3Gal]beta1,6GlcNAc and pNP-beta-GlcNAc-beta1,4-GalNAc substrates, respectively, as well as beta-1,2-linked N-acetylglucosamine units from the non-reducing end of N-glycans. Hydrolyzes GlcNAc residues linked to alpha1,3- or alpha1,6-mannose branch, but has low activity on substrates with more than one GlcNAc residue on one of the mannose branches. Releases terminal GlcNAc moieties from the N-glycopeptide Gly-Glu-Asn-(GlcNAc2Man3GlcNAc2)-Arg with high efficiency. Has moderate hydrolytic activity on the chitobiose moiety of N-glycopeptide substrate Gly-Glu-Asn-(GlcNAc2)-Arg. Does not hydrolyze GlcNAc residues from N-glycan structures bearing a bisecting GlcNAc moiety (beta1,4-linked GlcNAc to the beta1,4-linked core mannose) (PubMed:29304441). Potentially capable of cleaving the specific glycoside linkages in the process of mucin degradation in human intestinal tract (Probable). Hydrolyzes synthetic substrate pNP-beta-GlcNAc with high activity and pNP-beta-GalNAc to a lesser extent (PubMed:29304441, PubMed:30846208). Does not hydrolyze pNP-beta-glucose, pNP-beta-galactose, pNP-alpha-glucose, pNP-alpha-galactose, pNP-alpha-GlcNAc or pNP-alpha-fucose (PubMed:29304441).<ref>PMID:29304441</ref> <ref>PMID:30846208</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
beta-N-acetylhexosaminidases from Akkermansia muciniphila was reported to perform the crystal structure with GlcNAc complex, which proved to be the substrate of Am2301. Domain II of Am2301 is consisted of amino acid residues 111-489 and is folded as a (beta/alpha)8 barrel with the active site combined of the glycosyl hydrolases. Crystallographic evidence showed that Asp-278 and Glu-279 could be the catalytic site and Tyr-373 may plays a role on binding the substrate. Moreover, Am2301 prefers to bind Zn ion, which similar to other GH 20 family. Enzyme activity and kinetic parameters of wild-type Am2301 and mutants proved that Asp-278 and Glu-279 are the catalytic sites and they play a critical role on the catalytic process. Overall, our results demonstrate that Am2301 and its complex with GlcNAC provide obvious structural evidence for substrate-assisted catalysis. Obviously, this expands our understanding on the mode of substrate-assisted reaction for this enzyme family in Akkermansia muciniphila. | |||
Crystallographic evidence for substrate-assisted catalysis of beta-N-acetylhexosaminidas from Akkermansia muciniphila.,Chen X, Wang J, Liu M, Yang W, Wang Y, Tang R, Zhang M Biochem Biophys Res Commun. 2019 Apr 16;511(4):833-839. doi:, 10.1016/j.bbrc.2019.02.074. Epub 2019 Mar 4. PMID:30846208<ref>PMID:30846208</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6jeb" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Beta-N-acetylhexosaminidase 3D structures|Beta-N-acetylhexosaminidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Akkermansia muciniphila ATCC BAA-835]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Chen | [[Category: Chen X]] | ||
[[Category: Liu | [[Category: Liu MJ]] | ||
[[Category: Tang | [[Category: Tang RP]] | ||
[[Category: Wang | [[Category: Wang JC]] | ||
[[Category: Wang | [[Category: Wang YZ]] | ||
[[Category: Yang | [[Category: Yang WY]] | ||
[[Category: Zhang | [[Category: Zhang M]] | ||