4gyj

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==Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1)==
==Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1)==
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<StructureSection load='4gyj' size='340' side='right' caption='[[4gyj]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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<StructureSection load='4gyj' size='340' side='right'caption='[[4gyj]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4gyj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GYJ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4gyj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GYJ 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=MUB:N-ACETYLMURAMIC+ACID'>MUB</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.65&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gyk|4gyk]]</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=MUB:N-ACETYLMURAMIC+ACID'>MUB</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU01660, NagZ, ybbD, yzbA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=4gyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gyj OCA], [https://pdbe.org/4gyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gyj RCSB], [https://www.ebi.ac.uk/pdbsum/4gyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gyj 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=4gyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gyj OCA], [http://pdbe.org/4gyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gyj RCSB], [http://www.ebi.ac.uk/pdbsum/4gyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gyj 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/NAGZ_BACSU NAGZ_BACSU] 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. Cleaves muropeptides, but not peptidoglycan.<ref>PMID:20400549</ref> <ref>PMID:20826810</ref>
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NagZ is a glycoside hydrolase that participates in peptidoglycan (PG) recycling by removing beta-N-acetylglucosamine from PG fragments that are excised from the bacterial cell wall during growth. Notably, the products formed by NagZ, 1,6-anhydroMurNAc-peptides, activate beta-lactam resistance in many Gram-negative bacteria, making this enzyme of interest as a potential therapeutic target. Crystal structure determinations of NagZ from Salmonella typhimurium and Bacillus subtilis in complex with natural substrate, trapped as a glycosyl-enzyme intermediate, and bound to product, define the reaction coordinate of the NagZ family of enzymes. The structures, combined with kinetic studies, reveal an uncommon degree of structural plasticity within the active site of a glycoside hydrolase, and unveil how NagZ drives substrate distortion using a highly mobile loop that contains a conserved histidine that has been proposed as the general acid/base.
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Active Site Plasticity within the Glycoside Hydrolase NagZ Underlies a Dynamic Mechanism of Substrate Distortion.,Bacik JP, Whitworth GE, Stubbs KA, Vocadlo DJ, Mark BL Chem Biol. 2012 Nov 21;19(11):1471-82. doi: 10.1016/j.chembiol.2012.09.016. PMID:23177201<ref>PMID:23177201</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 4gyj" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacsu]]
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[[Category: Bacillus subtilis subsp. subtilis str. 168]]
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[[Category: Bacik, J P]]
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[[Category: Large Structures]]
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[[Category: Mark, B L]]
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[[Category: Bacik JP]]
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[[Category: Hydrolase]]
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[[Category: Mark BL]]
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[[Category: Hydrolase-substrate complex]]
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[[Category: Tim-barrel]]
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Current revision

Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1)

PDB ID 4gyj

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