3zqd: Difference between revisions

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[[~~Image~~:~~3zqd~~.~~jpg~~|~~left~~|~~200px~~]]

==B. subtilis L,D-transpeptidase==

== Structural highlights ==

<table><tr><td colspan='2'>[[3zqd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis Bacillus subtilis subsp. subtilis]. 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>

</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1y7m|1y7m]]</td></tr>

<tr><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://www.rcsb.org/pdb/explore.do?structureId=3zqd RCSB], [http://www.ebi.ac.uk/pdbsum/3zqd PDBsum]</span></td></tr>

<table>

== 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.

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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<ref>PMID:22579252</ref>

~~The line below this paragraph~~, ~~containing "STRUCTURE_3zqd"~~, ~~creates the "~~Structure ~~Box" on the page~~.

~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~

~~or the SCENE parameter~~ (~~which sets the initial scene displayed when the page is loaded~~),

~~or leave the SCENE parameter empty for the default display~~.

-->

~~{{STRUCTURE_3zqd| PDB=3zqd | SCENE= }}~~

~~===B. subtilis L~~,~~D-transpeptidase===~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

~~<!--~~

~~The line below this paragraph, {{ABSTRACT_PUBMED_22579252}}, adds~~ the ~~Publication Abstract to the page~~

__TOC__

~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22579252 is the PubMed ID number~~.

</StructureSection>

-->

~~{{ABSTRACT_PUBMED_22579252}}~~

~~==About this Structure==~~

~~[[3zqd]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis Bacillus subtilis subsp. subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZQD OCA].~~

==~~Reference~~==

<~~ref group="xtra">PMID:022579252<~~/~~ref~~><~~ref group="xtra">PMID:016287140</ref><references group="xtra"~~/>

[[Category: Bacillus subtilis subsp. subtilis]]

[[Category: Arthur, M.]]

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@@ Line 1: / Line 1: @@
-[[Image:3zqd.jpg|left|200px]]
+==B. subtilis L,D-transpeptidase==
+<StructureSection load='3zqd' size='340' side='right' caption='[[3zqd]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3zqd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis Bacillus subtilis subsp. subtilis]. 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>
+</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1y7m|1y7m]]</td></tr>
+<tr><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://www.rcsb.org/pdb/explore.do?structureId=3zqd RCSB], [http://www.ebi.ac.uk/pdbsum/3zqd PDBsum]</span></td></tr>
+<table>
+<div style="background-color:#fffaf0;">
+== 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) &gt; 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<ref>PMID:22579252</ref>
-The line below this paragraph, containing "STRUCTURE_3zqd", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_3zqd|  PDB=3zqd  |  SCENE=  }}
-===B. subtilis L,D-transpeptidase===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_22579252}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 22579252 is the PubMed ID number.
+</StructureSection>
--->
-{{ABSTRACT_PUBMED_22579252}}
-==About this Structure==
-[[3zqd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis Bacillus subtilis subsp. subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZQD OCA].
-==Reference==
-<ref group="xtra">PMID:022579252</ref><ref group="xtra">PMID:016287140</ref><references group="xtra"/>
 [[Category: Bacillus subtilis subsp. subtilis]]
 [[Category: Arthur, M.]]