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| | ==Structure of YBBD in complex with pugnac== | | ==Structure of YBBD in complex with pugnac== |
| - | <StructureSection load='3nvd' size='340' side='right' caption='[[3nvd]], [[Resolution|resolution]] 1.84Å' scene=''> | + | <StructureSection load='3nvd' size='340' side='right'caption='[[3nvd]], [[Resolution|resolution]] 1.84Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3nvd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3cqm 3cqm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NVD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3nvd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3cqm 3cqm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NVD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OAN:O-(2-ACETAMIDO-2-DEOXY+D-GLUCOPYRANOSYLIDENE)+AMINO-N-PHENYLCARBAMATE'>OAN</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.836Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bmx|3bmx]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OAN:O-(2-ACETAMIDO-2-DEOXY+D-GLUCOPYRANOSYLIDENE)+AMINO-N-PHENYLCARBAMATE'>OAN</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ybbD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3nvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nvd OCA], [https://pdbe.org/3nvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nvd RCSB], [https://www.ebi.ac.uk/pdbsum/3nvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nvd ProSAT]</span></td></tr> |
| - | <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>
| + | |
| - | <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=3nvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nvd OCA], [http://pdbe.org/3nvd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nvd RCSB], [http://www.ebi.ac.uk/pdbsum/3nvd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nvd 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> |
| | == 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: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Beta-N-acetylhexosaminidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Diederichs, K]] | + | [[Category: Diederichs K]] |
| - | [[Category: Bacillus subtili]]
| + | |
| - | [[Category: Beta-n-hexosaminidase]]
| + | |
| - | [[Category: Glycosidase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Lipoprotein]]
| + | |
| - | [[Category: Membrane]]
| + | |
| - | [[Category: Palmitate]]
| + | |
| - | [[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]
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
Three-dimensional structures of NagZ of Bacillus subtilis, the first structures of a two-domain beta-N-acetylglucosaminidase of family 3 of glycosidases, were determined with and without the transition state mimicking inhibitor PUGNAc bound to the active site, at 1.84- and 1.40-A resolution, respectively. The structures together with kinetic analyses of mutants revealed an Asp-His dyad involved in catalysis: His(234) of BsNagZ acts as general acid/base catalyst and is hydrogen bonded by Asp(232) for proper function. Replacement of both His(234) and Asp(232) with glycine reduced the rate of hydrolysis of the fluorogenic substrate 4'-methylumbelliferyl N-acetyl-beta-D-glucosaminide 1900- and 4500-fold, respectively, and rendered activity pH-independent in the alkaline range consistent with a role of these residues in acid/base catalysis. N-Acetylglucosaminyl enzyme intermediate accumulated in the H234G mutant and beta-azide product was formed in the presence of sodium azide in both mutants. The Asp-His dyad is conserved within beta-N-acetylglucosaminidases but otherwise absent in beta-glycosidases of family 3, which instead carry a "classical" glutamate acid/base catalyst. The acid/base glutamate of Hordeum vulgare exoglucanase (Exo1) superimposes with His(234) of the dyad of BsNagZ and, in contrast to the latter, protrudes from a second domain of the enzyme into the active site. This is the first report of an Asp-His catalytic dyad involved in hydrolysis of glycosides resembling in function the Asp-His-Ser triad of serine proteases. Our findings will facilitate the development of mechanism-based inhibitors that selectively target family 3 beta-N-acetylglucosaminidases, which are involved in bacterial cell wall turnover, spore germination, and induction of beta-lactamase.
Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism.,Litzinger S, Fischer S, Polzer P, Diederichs K, Welte W, Mayer C J Biol Chem. 2010 Nov 12;285(46):35675-84. Epub 2010 Sep 7. PMID:20826810[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
- ↑ 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
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