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5o6y

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==Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide==
==Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide==
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<StructureSection load='5o6y' size='340' side='right' caption='[[5o6y]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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<StructureSection load='5o6y' size='340' side='right'caption='[[5o6y]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5o6y]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O6Y FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5o6y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_ATCC_14579 Bacillus cereus ATCC 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O6Y 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=5YA:4-NAPHTHALEN-1-YL-~{N}-OXIDANYL-BENZAMIDE'>5YA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.498&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXU:2-HYDROXY-L-PROLINE'>PXU</scene></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=5YA:4-NAPHTHALEN-1-YL-~{N}-OXIDANYL-BENZAMIDE'>5YA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=PXU:2-HYDROXY-L-PROLINE'>PXU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4l1g|4l1g]]</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=5o6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o6y OCA], [https://pdbe.org/5o6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o6y RCSB], [https://www.ebi.ac.uk/pdbsum/5o6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o6y 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=5o6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o6y OCA], [http://pdbe.org/5o6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o6y RCSB], [http://www.ebi.ac.uk/pdbsum/5o6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o6y 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/PGDA1_BACCR PGDA1_BACCR] Catalyzes the deacetylation of N-acetylglucosamine (GlcNAc) residues in peptidoglycan (PubMed:15961396, PubMed:29983281). Also acts on soluble chitin substrates and N-acetylchitooligomers. Acts on cell wall peptidoglycan from the Gram-positive bacteria B.cereus and B.subtilis and the Gram-negative bacterium H.pylori. Not active on acetylated xylan (PubMed:15961396).<ref>PMID:15961396</ref> <ref>PMID:29983281</ref>
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The full extent of proline (Pro) hydroxylation has yet to be established, as it is largely unexplored in bacteria. We describe here a so far unknown Pro hydroxylation activity which occurs in active sites of polysaccharide deacetylases (PDAs) from bacterial pathogens, modifying the protein backbone at the Calpha atom of a Pro residue to produce 2-hydroxyproline (2-Hyp). This process modifies with high specificity a conserved Pro, shares with the deacetylation reaction the same active site and one cata-lytic residue and utilizes molecular oxygen as source for the hydroxyl group oxygen of 2-Hyp. By providing additional hydrogen bonding capacity, the Pro--&gt;2-Hyp conversion alters the active site and enhances significantly deacetylase activity, probably by creating a more favorable environment for transition state stabilization. Our results classify this process as an active site "maturation", which is highly atypical by being a protein backbone modifying activity, rather than a side-chain modifying one.
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An unusual alpha-carbon hydroxylation of proline promotes active-site maturation.,Fadouloglou VE, Balomenou S, Aivaliotis M, Kotsifaki D, Arnaouteli S, Tomatsidou A, Efstathiou G, Kountourakis N, Miliara S, Griniezaki M, Tsalafouta A, Pergantis SA, Boneca IG, Glykos NM, Bouriotis V, Kokkinidis M J Am Chem Soc. 2017 Mar 23. doi: 10.1021/jacs.6b12209. PMID:28333455<ref>PMID:28333455</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 5o6y" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Fadouloglou, V E]]
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[[Category: Bacillus cereus ATCC 14579]]
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[[Category: Kokkinidis, M]]
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[[Category: Large Structures]]
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[[Category: Kotsifaki, D]]
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[[Category: Fadouloglou VE]]
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[[Category: Complex]]
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[[Category: Kokkinidis M]]
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[[Category: Deacetylase]]
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[[Category: Kotsifaki D]]
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[[Category: Hydrolase]]
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[[Category: Inhibitor]]
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[[Category: Peptidoglycan]]
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Current revision

Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide

PDB ID 5o6y

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