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| | ==Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1211)== | | ==Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1211)== |
| - | <StructureSection load='4gyk' size='340' side='right' caption='[[4gyk]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='4gyk' size='340' side='right'caption='[[4gyk]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4gyk]] 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=4GYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GYK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4gyk]] 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=4GYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GYK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | + | </td></tr><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> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MUB:N-ACETYLMURAMIC+ACID'>MUB</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=4gyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gyk OCA], [https://pdbe.org/4gyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gyk RCSB], [https://www.ebi.ac.uk/pdbsum/4gyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gyk ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gyj|4gyj]]</td></tr>
| + | |
| - | <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>
| + | |
| - | <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=4gyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gyk OCA], [http://pdbe.org/4gyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gyk RCSB], [http://www.ebi.ac.uk/pdbsum/4gyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gyk ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Bacik, J P]] | + | [[Category: Large Structures]] |
| - | [[Category: Mark, B L]] | + | [[Category: Bacik JP]] |
| - | [[Category: Hydrolase]] | + | [[Category: Mark BL]] |
| - | [[Category: Hydrolase-substrate complex]]
| + | |
| - | [[Category: Tim-barrel]]
| + | |
| Structural highlights
Function
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.[1] [2]
Publication Abstract from PubMed
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.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Litzinger S, Duckworth A, Nitzsche K, Risinger C, Wittmann V, Mayer C. Muropeptide rescue in Bacillus subtilis involves sequential hydrolysis by beta-N-acetylglucosaminidase and N-acetylmuramyl-L-alanine amidase. J Bacteriol. 2010 Jun;192(12):3132-43. doi: 10.1128/JB.01256-09. Epub 2010 Apr, 16. PMID:20400549 doi:http://dx.doi.org/10.1128/JB.01256-09
- ↑ Litzinger S, Fischer S, Polzer P, Diederichs K, Welte W, Mayer C. Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism. J Biol Chem. 2010 Nov 12;285(46):35675-84. Epub 2010 Sep 7. PMID:20826810 doi:10.1074/jbc.M110.131037
- ↑ Bacik JP, Whitworth GE, Stubbs KA, Vocadlo DJ, Mark BL. Active Site Plasticity within the Glycoside Hydrolase NagZ Underlies a Dynamic Mechanism of Substrate Distortion. Chem Biol. 2012 Nov 21;19(11):1471-82. doi: 10.1016/j.chembiol.2012.09.016. PMID:23177201 doi:10.1016/j.chembiol.2012.09.016
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