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| | ==B. subtilis L,D-transpeptidase== | | ==B. subtilis L,D-transpeptidase== |
| - | <StructureSection load='3zqd' size='340' side='right' caption='[[3zqd]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='3zqd' size='340' side='right'caption='[[3zqd]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3zqd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZQD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3zqd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZQD FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1y7m|1y7m]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=3zqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zqd OCA], [http://pdbe.org/3zqd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zqd RCSB], [http://www.ebi.ac.uk/pdbsum/3zqd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zqd 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=3zqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zqd OCA], [https://pdbe.org/3zqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zqd RCSB], [https://www.ebi.ac.uk/pdbsum/3zqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zqd ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/YKUD_BACSU YKUD_BACSU]] Probable enzyme that may play an important role in cell wall biology.<ref>PMID:16287140</ref> | + | [https://www.uniprot.org/uniprot/YKUD_BACSU YKUD_BACSU] Probable enzyme that may play an important role in cell wall biology.<ref>PMID:16287140</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: Arthur, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Bougault, C]] | + | [[Category: Arthur M]] |
| - | [[Category: Hugonnet, J E]] | + | [[Category: Bougault C]] |
| - | [[Category: Lecoq, L]] | + | [[Category: Hugonnet J-E]] |
| - | [[Category: Pessey, O]] | + | [[Category: Lecoq L]] |
| - | [[Category: Simorre, J P]] | + | [[Category: Pessey O]] |
| - | [[Category: Veckerle, C]] | + | [[Category: Simorre J-P]] |
| - | [[Category: Antibiotic resistance]]
| + | [[Category: Veckerle C]] |
| - | [[Category: Cysteine protease]]
| + | |
| - | [[Category: Peptidoglycan]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
YKUD_BACSU Probable enzyme that may play an important role in cell wall biology.[1]
Publication Abstract from PubMed
beta-lactams inhibit peptidoglycan polymerization by acting as suicide substrates of essential d,d-transpeptidases. Bypass of these enzymes by unrelated l,d-transpeptidases results in beta-lactam resistance, although carbapenems remain unexpectedly active. To gain insight into carbapenem specificity of l,d-transpeptidases (Ldts), we solved the nuclear magnetic resonance (NMR) structures of apo and imipenem-acylated Bacillus subtilis Ldt and show that the cysteine nucleophile is present as a neutral imidazole-sulfhydryl pair in the substrate-free enzyme. NMR relaxation dispersion does not reveal any preexisting conformational exchange in the apoenzyme, and change in flexibility is not observed upon noncovalent binding of beta-lactams (K(D) > 37.5 mM). In contrast, covalent modification of active cysteine by both carbapenems and 2-nitro-5-thiobenzoate induces backbone flexibility that does not result from disruption of the imidazole-sulfhydryl proton interaction or steric hindrance. The chemical step of the reaction determines enzyme specificity since no differences in drug affinity were observed.
Dynamics Induced by beta-Lactam Antibiotics in the Active Site of Bacillus subtilisl,d-Transpeptidase.,Lecoq L, Bougault C, Hugonnet JE, Veckerle C, Pessey O, Arthur M, Simorre JP Structure. 2012 May 9;20(5):850-61. PMID:22579252[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bielnicki J, Devedjiev Y, Derewenda U, Dauter Z, Joachimiak A, Derewenda ZS. B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes. Proteins. 2006 Jan 1;62(1):144-51. PMID:16287140 doi:10.1002/prot.20702
- ↑ Lecoq L, Bougault C, Hugonnet JE, Veckerle C, Pessey O, Arthur M, Simorre JP. Dynamics Induced by beta-Lactam Antibiotics in the Active Site of Bacillus subtilisl,d-Transpeptidase. Structure. 2012 May 9;20(5):850-61. PMID:22579252 doi:10.1016/j.str.2012.03.015
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