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5wzr

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==Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex==
==Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex==
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<StructureSection load='5wzr' size='340' side='right' caption='[[5wzr]], [[Resolution|resolution]] 2.79&Aring;' scene=''>
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<StructureSection load='5wzr' size='340' side='right'caption='[[5wzr]], [[Resolution|resolution]] 2.79&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5wzr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WZR FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5wzr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WZR FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DJN:N-[(3S,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)PIPERIDIN-3-YL]ACETAMIDE'>DJN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.79&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wzn|5wzn]], [[5wzp|5wzp]], [[5wzq|5wzq]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DJN:N-[(3S,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)PIPERIDIN-3-YL]ACETAMIDE'>DJN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-N-acetylgalactosaminidase Alpha-N-acetylgalactosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.49 3.2.1.49] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5wzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wzr OCA], [https://pdbe.org/5wzr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wzr RCSB], [https://www.ebi.ac.uk/pdbsum/5wzr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wzr ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5wzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wzr OCA], [http://pdbe.org/5wzr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wzr RCSB], [http://www.ebi.ac.uk/pdbsum/5wzr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wzr ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/G5ELM1_BIFBI G5ELM1_BIFBI]
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The alpha-N-acetylgalactosaminidase from the probiotic bacterium Bifidobacterium bifidum (NagBb) belongs to the glycoside hydrolase family 129 and hydrolyzes the glycosidic bond of Tn-antigen (GalNAcalpha1-Ser/Thr). NagBb is involved in assimilation of O-glycans on mucin glycoproteins by B. bifidum in the human gastrointestinal tract, but its catalytic mechanism has remained elusive because of a lack of sequence homology around putative catalytic residues and of other structural information. Here we report the X-ray crystal structure of NagBb, representing the first GH129 family structure, solved by the single-wavelength anomalous dispersion method based on sulfur atoms of the native protein. We determined ligand-free, GalNAc, and inhibitor complex forms of NagBb and found that Asp-435 and Glu-478 are located in the catalytic domain at appropriate positions for direct nucleophilic attack at the anomeric carbon and proton donation for the glycosidic bond oxygen, respectively. A highly conserved Asp-330 forms a hydrogen bond with the O4 hydroxyl of GalNAc in the -1 subsite, and Trp-398 provides a stacking platform for the GalNAc pyranose ring. Interestingly, a metal ion, presumably Ca2+, is involved in the recognition of the GalNAc N-acetyl group. Mutations at Asp-435, Glu-478, Asp-330, and Trp-398 and residues involved in metal coordination (including an all-Ala quadruple mutant) significantly reduced the activity, indicating that these residues and the metal ion play important roles in substrate recognition and catalysis. Interestingly, NagBb exhibited some structural similarities to the GH101 endo-alpha-N-acetylgalactosaminidases, but several critical differences in substrate recognition and reaction mechanism account for the different activities of these two enzymes.
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The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors.,Sato M, Liebschner D, Yamada Y, Matsugaki N, Arakawa T, Wills SS, Hattie M, Stubbs KA, Ito T, Senda T, Ashida H, Fushinobu S J Biol Chem. 2017 Jul 21;292(29):12126-12138. doi: 10.1074/jbc.M117.777391. Epub , 2017 May 25. PMID:28546425<ref>PMID:28546425</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5wzr" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Alpha-N-acetylgalactosaminidase]]
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[[Category: Bifidobacterium bifidum]]
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[[Category: Arakawa, T]]
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[[Category: Large Structures]]
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[[Category: Ashida, H]]
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[[Category: Arakawa T]]
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[[Category: Fushinobu, S]]
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[[Category: Ashida H]]
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[[Category: Sato, M]]
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[[Category: Fushinobu S]]
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[[Category: Glycoside hydrolase]]
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[[Category: Sato M]]
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[[Category: Hydrolase]]
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Current revision

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex

PDB ID 5wzr

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