This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3zqd

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3zqd"

@@ 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

From Proteopedia

Current revision

B. subtilis L,D-transpeptidase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox