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| | <StructureSection load='3gs6' size='340' side='right'caption='[[3gs6]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='3gs6' size='340' side='right'caption='[[3gs6]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3gs6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GS6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3gs6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GS6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NP6:[[(3R,4R,5S,6R)-3-(BUTANOYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>NP6</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2oxn|2oxn]], [[1tr9|1tr9]], [[1y65|1y65]], [[3gsm|3gsm]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NP6:[[(3R,4R,5S,6R)-3-(BUTANOYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)OXAN-2-YLIDENE]AMINO]+N-PHENYLCARBAMATE'>NP6</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nagZ, VC_0692 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </span></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=3gs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gs6 OCA], [https://pdbe.org/3gs6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gs6 RCSB], [https://www.ebi.ac.uk/pdbsum/3gs6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gs6 ProSAT]</span></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=3gs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gs6 OCA], [https://pdbe.org/3gs6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gs6 RCSB], [https://www.ebi.ac.uk/pdbsum/3gs6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gs6 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/NAGZ_VIBCH NAGZ_VIBCH]] 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. Plays a role in beta-lactam antibiotic resistance via its role in generating anhydro-N-acetylmuramic acid-linked peptides; these peptides function as signaling molecules that induce high-level expression of the beta-lactamase AmpC.<ref>PMID:24009110</ref> <ref>PMID:17439950</ref> <ref>PMID:19499593</ref>
| + | [https://www.uniprot.org/uniprot/NAGZ_VIBCH NAGZ_VIBCH] 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. Plays a role in beta-lactam antibiotic resistance via its role in generating anhydro-N-acetylmuramic acid-linked peptides; these peptides function as signaling molecules that induce high-level expression of the beta-lactamase AmpC.<ref>PMID:24009110</ref> <ref>PMID:17439950</ref> <ref>PMID:19499593</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillo virgola del koch trevisan 1884]] | |
| - | [[Category: Beta-N-acetylhexosaminidase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Balcewich, M D]] | + | [[Category: Vibrio cholerae]] |
| - | [[Category: Mark, B L]] | + | [[Category: Balcewich MD]] |
| - | [[Category: Cell cycle]] | + | [[Category: Mark BL]] |
| - | [[Category: Cell division]]
| + | |
| - | [[Category: Cell shape]]
| + | |
| - | [[Category: Cell wall biogenesis/degradation]]
| + | |
| - | [[Category: Glycosidase]]
| + | |
| - | [[Category: Glycoside hydrolase family 3]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Peptidoglycan synthesis]]
| + | |
| Structural highlights
Function
NAGZ_VIBCH 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. Plays a role in beta-lactam antibiotic resistance via its role in generating anhydro-N-acetylmuramic acid-linked peptides; these peptides function as signaling molecules that induce high-level expression of the beta-lactamase AmpC.[1] [2] [3]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
NagZ is an exo-N-acetyl-beta-glucosaminidase, found within Gram-negative bacteria, that acts in the peptidoglycan recycling pathway to cleave N-acetylglucosamine residues off peptidoglycan fragments. This activity is required for resistance to cephalosporins mediated by inducible AmpC beta-lactamase. NagZ uses a catalytic mechanism involving a covalent glycosyl enzyme intermediate, unlike that of the human exo-N-acetyl-beta-glucosaminidases: O-GlcNAcase and the beta-hexosaminidase isoenzymes. These latter enzymes, which remove GlcNAc from glycoconjugates, use a neighboring-group catalytic mechanism that proceeds through an oxazoline intermediate. Exploiting these mechanistic differences we previously developed 2-N-acyl derivatives of O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc), which selectively inhibits NagZ over the functionally related human enzymes and attenuate antibiotic resistance in Gram-negatives that harbor inducible AmpC. To understand the structural basis for the selectivity of these inhibitors for NagZ, we have determined its crystallographic structure in complex with N-valeryl-PUGNAc, the most selective known inhibitor of NagZ over both the human beta-hexosaminidases and O-GlcNAcase. The selectivity stems from the five-carbon acyl chain of N-valeryl-PUGNAc, which we found ordered within the enzyme active site. In contrast, a structure determination of a human O-GlcNAcase homologue bound to a related inhibitor N-butyryl-PUGNAc, which bears a four-carbon chain and is selective for both NagZ and O-GlcNAcase over the human beta-hexosamnidases, reveals that this inhibitor induces several conformational changes in the active site of this O-GlcNAcase homologue. A comparison of these complexes, and with the human beta-hexosaminidases, reveals how selectivity for NagZ can be engineered by altering the 2-N-acyl substituent of PUGNAc to develop inhibitors that repress AmpC mediated beta-lactam resistance.
Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: Structural basis for selective inhibition of the glycoside hydrolase NagZ.,Balcewich MD, Stubbs KA, He Y, James TW, Davies GJ, Vocadlo DJ, Mark BL Protein Sci. 2009 Apr 16. PMID:19499593[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Stubbs KA, Bacik JP, Perley-Robertson GE, Whitworth GE, Gloster TM, Vocadlo DJ, Mark BL. The Development of Selective Inhibitors of NagZ: Increased Susceptibility of Gram-Negative Bacteria to beta-Lactams. Chembiochem. 2013 Oct 11;14(15):1973-81. doi: 10.1002/cbic.201300395. Epub 2013, Sep 5. PMID:24009110 doi:http://dx.doi.org/10.1002/cbic.201300395
- ↑ Stubbs KA, Balcewich M, Mark BL, Vocadlo DJ. Small molecule inhibitors of a glycoside hydrolase attenuate inducible AmpC-mediated beta-lactam resistance. J Biol Chem. 2007 Jul 20;282(29):21382-91. Epub 2007 Apr 16. PMID:17439950 doi:10.1074/jbc.M700084200
- ↑ Balcewich MD, Stubbs KA, He Y, James TW, Davies GJ, Vocadlo DJ, Mark BL. Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: Structural basis for selective inhibition of the glycoside hydrolase NagZ. Protein Sci. 2009 Apr 16. PMID:19499593 doi:10.1002/pro.137
- ↑ Balcewich MD, Stubbs KA, He Y, James TW, Davies GJ, Vocadlo DJ, Mark BL. Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: Structural basis for selective inhibition of the glycoside hydrolase NagZ. Protein Sci. 2009 Apr 16. PMID:19499593 doi:10.1002/pro.137
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