3zqd: Difference between revisions

Revision as of 10:07, 14 June 2023

B. subtilis L,D-transpeptidase

Structural highlights

3zqd is a 1 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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

[2] 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

[1]

[2]

@@ Line 1: / Line 1: @@
 ==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 ==
-<table><tr><td colspan='2'>[[3zqd]] is a 1 chain structure with sequence from [https://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 [https://proteopedia.org/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"><div style='overflow: auto; max-height: 3em;'>[[1y7m|1y7m]]</div></td></tr>
+</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>
-<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>
 == Function ==
-[[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>
+[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;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Bacsu]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
 [[Category: Large Structures]]
-[[Category: Arthur, M]]
+[[Category: Arthur M]]
-[[Category: Bougault, C]]
+[[Category: Bougault C]]
-[[Category: Hugonnet, J E]]
+[[Category: Hugonnet J-E]]
-[[Category: Lecoq, L]]
+[[Category: Lecoq L]]
-[[Category: Pessey, O]]
+[[Category: Pessey O]]
-[[Category: Simorre, J P]]
+[[Category: Simorre J-P]]
-[[Category: Veckerle, C]]
+[[Category: Veckerle C]]
-[[Category: Antibiotic resistance]]
-[[Category: Cysteine protease]]
-[[Category: Peptidoglycan]]
-[[Category: Transferase]]

3zqd: Difference between revisions

Revision as of 10:07, 14 June 2023

B. subtilis L,D-transpeptidase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools