6z2o: Difference between revisions

Latest revision as of 13:40, 24 January 2024

Crystal structure of wild type OgpA from Akkermansia muciniphila in P 21 21 21

Structural highlights

6z2o is a 1 chain structure with sequence from Akkermansia muciniphila ATCC BAA-835. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.649Å
Ligands:	EDO, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B2UR60_AKKM8

Publication Abstract from PubMed

Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila, an O-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also contribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins.

Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila.,Trastoy B, Naegeli A, Anso I, Sjogren J, Guerin ME Nat Commun. 2020 Sep 24;11(1):4844. doi: 10.1038/s41467-020-18696-y. PMID:32973204^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Trastoy B, Naegeli A, Anso I, Sjogren J, Guerin ME. Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila. Nat Commun. 2020 Sep 24;11(1):4844. doi: 10.1038/s41467-020-18696-y. PMID:32973204 doi:https://dx.doi.org/10.1038/s41467-020-18696-y

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OCA

[1] Trastoy B, Naegeli A, Anso I, Sjogren J, Guerin ME. Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila. Nat Commun. 2020 Sep 24;11(1):4844. doi: 10.1038/s41467-020-18696-y. PMID:32973204 doi:https://dx.doi.org/10.1038/s41467-020-18696-y

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6z2o' size='340' side='right'caption='[[6z2o]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6z2o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Akkm8 Akkm8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z2O FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6z2o]] 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=6Z2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z2O FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 1.649&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Amuc_1119 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=349741 AKKM8])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=6z2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2o OCA], [https://pdbe.org/6z2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z2o RCSB], [https://www.ebi.ac.uk/pdbsum/6z2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2o ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/B2UR60_AKKM8 B2UR60_AKKM8]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Akkm8]]
+[[Category: Akkermansia muciniphila ATCC BAA-835]]
 [[Category: Large Structures]]
-[[Category: Anso, I]]
+[[Category: Anso I]]
-[[Category: Guerin, M E]]
+[[Category: Guerin ME]]
-[[Category: Naegali, A]]
+[[Category: Naegali A]]
-[[Category: Sjogren, J]]
+[[Category: Sjogren J]]
-[[Category: Trastoy, B]]
+[[Category: Trastoy B]]
-[[Category: Hydrolase]]
-[[Category: Mucin]]
-[[Category: O-glycan endopeptidase]]
-[[Category: Ogpa. metalloprotease]]

6z2o: Difference between revisions

Latest revision as of 13:40, 24 January 2024

Crystal structure of wild type OgpA from Akkermansia muciniphila in P 21 21 21

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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