7zui: Difference between revisions
New page: '''Unreleased structure''' The entry 7zui is ON HOLD Authors: Flanders, P.L., Contreras-Martel, C., Martins, A., Brown, N.W., Shirley, J.D., Nauta, K.M., Dessen, A., Carlson, E.E., Ambr... |
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==PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 5Az - Streptococcus pneumoniae R6== | |||
<StructureSection load='7zui' size='340' side='right'caption='[[7zui]], [[Resolution|resolution]] 1.57Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7zui]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZUI FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.57Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=K2O:6-azido-N-[(2R)-1-oxidanylidene-1-[[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]amino]propan-2-yl]hexanamide'>K2O</scene></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=7zui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zui OCA], [https://pdbe.org/7zui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zui RCSB], [https://www.ebi.ac.uk/pdbsum/7zui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zui ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q7CRA4_STRR6 Q7CRA4_STRR6] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
beta-Lactam antibiotics comprise one of the most widely used therapeutic classes to combat bacterial infections. This general scaffold has long been known to inhibit bacterial cell wall biosynthesis by inactivating penicillin-binding proteins (PBPs); however, bacterial resistance to beta-lactams is now widespread, and new strategies are urgently needed to target PBPs and other proteins involved in bacterial cell wall formation. A key requirement in the identification of strategies to overcome resistance is a deeper understanding of the roles of the PBPs and their associated proteins during cell growth and division, such as can be obtained with the use of selective chemical probes. Probe development has typically depended upon known PBP inhibitors, which have historically been thought to require a negatively charged moiety that mimics the C-terminus of the PBP natural peptidoglycan substrate, d-Ala-d-Ala. However, we have identified a new class of beta-lactone-containing molecules that interact with PBPs, often in an isoform-specific manner, and do not incorporate this C-terminal mimetic. Here, we report a series of structural biology experiments and molecular dynamics simulations that we utilized to evaluate specific binding modes of this novel PBP inhibitor class. In this work, we obtained <2 A resolution X-ray structures of four beta-lactone probes bound to PBP1b from Streptococcus pneumoniae. Despite their diverging recognition modes beyond the site of covalent modification, these four probes all efficiently labeled PBP1b, as well as other PBPs from S. pneumoniae. From these structures, we analyzed protein-ligand interactions and characterized the beta-lactone-bound active sites using in silico mutagenesis and molecular dynamics. Our approach has clarified the dynamic interaction profile in this series of ligands, expanding the understanding of PBP inhibitor binding. | |||
Combined Structural Analysis and Molecular Dynamics Reveal Penicillin-Binding Protein Inhibition Mode with beta-Lactones.,Flanders PL, Contreras-Martel C, Brown NW, Shirley JD, Martins A, Nauta KN, Dessen A, Carlson EE, Ambrose EA ACS Chem Biol. 2022 Sep 29. doi: 10.1021/acschembio.2c00503. PMID:36173746<ref>PMID:36173746</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[ | </div> | ||
[[Category: | <div class="pdbe-citations 7zui" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]] | ||
[[Category: | == References == | ||
[[Category: Contreras-Martel | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: Flanders | </StructureSection> | ||
[[Category: Martins | [[Category: Large Structures]] | ||
[[Category: Streptococcus pneumoniae R6]] | |||
[[Category: Ambrose EA]] | |||
[[Category: Brown NW]] | |||
[[Category: Carlson EE]] | |||
[[Category: Contreras-Martel C]] | |||
[[Category: Dessen A]] | |||
[[Category: Flanders PL]] | |||
[[Category: Martins A]] | |||
[[Category: Nauta KM]] | |||
[[Category: Shirley JD]] | |||
Latest revision as of 16:34, 1 February 2024
PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 5Az - Streptococcus pneumoniae R6PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 5Az - Streptococcus pneumoniae R6
Structural highlights
FunctionPublication Abstract from PubMedbeta-Lactam antibiotics comprise one of the most widely used therapeutic classes to combat bacterial infections. This general scaffold has long been known to inhibit bacterial cell wall biosynthesis by inactivating penicillin-binding proteins (PBPs); however, bacterial resistance to beta-lactams is now widespread, and new strategies are urgently needed to target PBPs and other proteins involved in bacterial cell wall formation. A key requirement in the identification of strategies to overcome resistance is a deeper understanding of the roles of the PBPs and their associated proteins during cell growth and division, such as can be obtained with the use of selective chemical probes. Probe development has typically depended upon known PBP inhibitors, which have historically been thought to require a negatively charged moiety that mimics the C-terminus of the PBP natural peptidoglycan substrate, d-Ala-d-Ala. However, we have identified a new class of beta-lactone-containing molecules that interact with PBPs, often in an isoform-specific manner, and do not incorporate this C-terminal mimetic. Here, we report a series of structural biology experiments and molecular dynamics simulations that we utilized to evaluate specific binding modes of this novel PBP inhibitor class. In this work, we obtained <2 A resolution X-ray structures of four beta-lactone probes bound to PBP1b from Streptococcus pneumoniae. Despite their diverging recognition modes beyond the site of covalent modification, these four probes all efficiently labeled PBP1b, as well as other PBPs from S. pneumoniae. From these structures, we analyzed protein-ligand interactions and characterized the beta-lactone-bound active sites using in silico mutagenesis and molecular dynamics. Our approach has clarified the dynamic interaction profile in this series of ligands, expanding the understanding of PBP inhibitor binding. Combined Structural Analysis and Molecular Dynamics Reveal Penicillin-Binding Protein Inhibition Mode with beta-Lactones.,Flanders PL, Contreras-Martel C, Brown NW, Shirley JD, Martins A, Nauta KN, Dessen A, Carlson EE, Ambrose EA ACS Chem Biol. 2022 Sep 29. doi: 10.1021/acschembio.2c00503. PMID:36173746[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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