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| | <StructureSection load='5n1p' size='340' side='right'caption='[[5n1p]], [[Resolution|resolution]] 1.45Å' scene=''> | | <StructureSection load='5n1p' size='340' side='right'caption='[[5n1p]], [[Resolution|resolution]] 1.45Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5n1p]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N1P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N1P FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5n1p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N1P FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8GK:~{N}-oxidanylnaphthalene-1-carboxamide'>8GK</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.448Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BC_1974 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1396 ATCC 14579]), AT268_30040, B4155_0776, TQ94_03800, TU58_19865, WR51_09920, WR52_09510 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1396 ATCC 14579])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8GK:~{N}-oxidanylnaphthalene-1-carboxamide'>8GK</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5n1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n1p OCA], [http://pdbe.org/5n1p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n1p RCSB], [http://www.ebi.ac.uk/pdbsum/5n1p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n1p 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=5n1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n1p OCA], [https://pdbe.org/5n1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n1p RCSB], [https://www.ebi.ac.uk/pdbsum/5n1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n1p ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PGDA2_BACCR PGDA2_BACCR] Catalyzes the deacetylation of N-acetylglucosamine (GlcNAc) residues in peptidoglycan.<ref>PMID:29983281</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: Atcc 14579]] | |
| - | [[Category: Large Structures]] | |
| - | [[Category: Andreou, A]] | |
| - | [[Category: Eliopoulos, E E]] | |
| - | [[Category: Giastas, P]] | |
| | [[Category: Bacillus cereus]] | | [[Category: Bacillus cereus]] |
| - | [[Category: Ce4 domain]] | + | [[Category: Large Structures]] |
| - | [[Category: Hydrolase]] | + | [[Category: Andreou A]] |
| - | [[Category: Pgda]] | + | [[Category: Eliopoulos EE]] |
| - | [[Category: Polysaccharide deacetylase]] | + | [[Category: Giastas P]] |
| Structural highlights
5n1p is a 4 chain structure with sequence from Bacillus cereus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.448Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PGDA2_BACCR Catalyzes the deacetylation of N-acetylglucosamine (GlcNAc) residues in peptidoglycan.[1]
Publication Abstract from PubMed
The cell wall peptidoglycan is recognized as a primary target of the innate immune system, and usually its disintegration results in bacterial lysis. Bacillus cereus, a close relative of the highly virulent Bacillus anthracis, contains 10 polysaccharide deacetylases. Among these, the peptidoglycan N-acetylglucosamine deacetylase Bc1974 is the highest homologue to the Bacillus anthracis Ba1977 that is required for full virulence and is involved in resistance to the host's lysozyme. These metalloenzymes belong to the carbohydrate esterase family 4 (CE4) and are attractive targets for the development of new anti-infective agents. Herein we report the first X-ray crystal structures of the NodB domain of Bc1974, the conserved catalytic core of CE4s, in the unliganded form and in complex with four known metalloenzyme inhibitors and two amino acid hydroxamates that target the active site metal. These structures revealed the presence of two conformational states of a catalytic loop known as motif-4 (MT4), which were not observed previously for peptidoglycan deacetylases, but were recently shown in the structure of a Vibrio clolerae chitin deacetylase. By employing molecular docking of a substrate model, we describe a catalytic mechanism that probably involves initial binding of the substrate in a receptive, more open state of MT4 and optimal catalytic activity in the closed state of MT4, consistent with the previous observations. The ligand-bound structures presented here, in addition to the five Bc1974 inhibitors identified, provide a valuable basis for the design of antibacterial agents that target the peptidoglycan deacetylase Ba1977.
Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors.,Giastas P, Andreou A, Papakyriakou A, Koutsioulis D, Balomenou S, Tzartos SJ, Bouriotis V, Eliopoulos EE Biochemistry. 2018 Feb 6;57(5):753-763. doi: 10.1021/acs.biochem.7b00919. Epub, 2018 Jan 5. PMID:29257674[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Balomenou S, Koutsioulis D, Tomatsidou A, Tzanodaskalaki M, Petratos K, Bouriotis V. Polysaccharide deacetylases serve as new targets for the design of inhibitors against Bacillus anthracis and Bacillus cereus. Bioorg Med Chem. 2018 Jul 30;26(13):3845-3851. PMID:29983281 doi:10.1016/j.bmc.2018.06.045
- ↑ Giastas P, Andreou A, Papakyriakou A, Koutsioulis D, Balomenou S, Tzartos SJ, Bouriotis V, Eliopoulos EE. Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors. Biochemistry. 2018 Feb 6;57(5):753-763. doi: 10.1021/acs.biochem.7b00919. Epub, 2018 Jan 5. PMID:29257674 doi:http://dx.doi.org/10.1021/acs.biochem.7b00919
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