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5ly7

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==Crystal structure of NagZ H174A mutant from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin==
==Crystal structure of NagZ H174A mutant from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin==
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<StructureSection load='5ly7' size='340' side='right' caption='[[5ly7]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
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<StructureSection load='5ly7' size='340' side='right'caption='[[5ly7]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5ly7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LY7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LY7 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5ly7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LY7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LY7 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=NOK:2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN'>NOK</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 3.1&#8491;</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/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </span></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=NOK:2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN'>NOK</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=5ly7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ly7 OCA], [http://pdbe.org/5ly7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ly7 RCSB], [http://www.ebi.ac.uk/pdbsum/5ly7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ly7 ProSAT]</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=5ly7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ly7 OCA], [https://pdbe.org/5ly7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ly7 RCSB], [https://www.ebi.ac.uk/pdbsum/5ly7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ly7 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/NAGZ_PSEAE NAGZ_PSEAE]] Plays a role in peptidoglycan recycling by cleaving the terminal beta-1,4-linked N-acetylglucosamine (GlcNAc) from peptide-linked peptidoglycan fragments, giving rise to free GlcNAc, anhydro-N-acetylmuramic acid and anhydro-N-acetylmuramic acid-linked peptides.[HAMAP-Rule:MF_00364]
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[https://www.uniprot.org/uniprot/NAGZ_PSEAE NAGZ_PSEAE] Plays a role in peptidoglycan recycling by cleaving the terminal beta-1,4-linked N-acetylglucosamine (GlcNAc) from peptide-linked peptidoglycan fragments, giving rise to free GlcNAc, anhydro-N-acetylmuramic acid and anhydro-N-acetylmuramic acid-linked peptides.[HAMAP-Rule:MF_00364]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The N-acetylglucosaminidase NagZ of Pseudomonas aeruginosa catalyzes the first cytoplasmic step in recycling of muropeptides, cell-wall-derived natural products. This reaction regulates gene expression for the beta-lactam resistance enzyme, beta-lactamase. The enzyme catalyzes hydrolysis of N-acetyl-beta-d-glucosamine-(1--&gt;4)-1,6-anhydro-N-acetyl-beta-d-muramyl-peptide (1) to N-acetyl-beta-d-glucosamine (2) and 1,6-anhydro-N-acetyl-beta-d-muramyl-peptide (3). The structural and functional aspects of catalysis by NagZ were investigated by a total of seven X-ray structures, three computational models based on the X-ray structures, molecular-dynamics simulations and mutagenesis. The structural insights came from the unbound state and complexes of NagZ with the substrate, products and a mimetic of the transient oxocarbenium species, which were prepared by synthesis. The mechanism involves a histidine as acid/base catalyst, which is unique for glycosidases. The turnover process utilizes covalent modification of D244, requiring two transition-state species and is regulated by coordination with a zinc ion. The analysis provides a seamless continuum for the catalytic cycle, incorporating large motions by four loops that surround the active site.
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Catalytic Cycle of the N-Acetylglucosaminidase NagZ from Pseudomonas aeruginosa.,Acebron I, Mahasenan KV, De Benedetti S, Lee M, Artola-Recolons C, Hesek D, Wang H, Hermoso JA, Mobashery S J Am Chem Soc. 2017 May 10. doi: 10.1021/jacs.7b01626. PMID:28482153<ref>PMID:28482153</ref>
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==See Also==
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*[[Beta-Hexosaminidase|Beta-Hexosaminidase]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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*[[Beta-Hexosaminidase 3D structures|Beta-Hexosaminidase 3D structures]]
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</div>
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*[[Beta-N-acetylhexosaminidase 3D structures|Beta-N-acetylhexosaminidase 3D structures]]
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<div class="pdbe-citations 5ly7" 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: Beta-N-acetylhexosaminidase]]
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[[Category: Large Structures]]
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[[Category: Acebron, I]]
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[[Category: Pseudomonas aeruginosa PAO1]]
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[[Category: Artola-Recolons, C]]
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[[Category: Acebron I]]
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[[Category: Hermoso, J A]]
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[[Category: Artola-Recolons C]]
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[[Category: Mahasenan, K]]
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[[Category: Hermoso JA]]
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[[Category: Mobashery, S]]
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[[Category: Mahasenan K]]
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[[Category: Cell-wall recycling beta-hexosaminidase pseudomonas aeruginosa inhibitor]]
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[[Category: Mobashery S]]
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[[Category: Gene regulation]]
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Current revision

Crystal structure of NagZ H174A mutant from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin

PDB ID 5ly7

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