7o4b: Difference between revisions
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==Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with penicillin G== | ==Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with penicillin G== | ||
<StructureSection load='7o4b' size='340' side='right'caption='[[7o4b]]' scene=''> | <StructureSection load='7o4b' size='340' side='right'caption='[[7o4b]], [[Resolution|resolution]] 2.59Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O4B FirstGlance]. <br> | <table><tr><td colspan='2'>[[7o4b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_COL Staphylococcus aureus subsp. aureus COL]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O4B FirstGlance]. <br> | ||
</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=7o4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o4b OCA], [https://pdbe.org/7o4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o4b RCSB], [https://www.ebi.ac.uk/pdbsum/7o4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o4b ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.593Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=PNM:OPEN+FORM+-+PENICILLIN+G'>PNM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7o4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o4b OCA], [https://pdbe.org/7o4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o4b RCSB], [https://www.ebi.ac.uk/pdbsum/7o4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o4b ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0H2WVW5_STAAC A0A0H2WVW5_STAAC] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The penicillin-binding proteins are the enzyme catalysts of the critical transpeptidation crosslinking polymerization reaction of bacterial peptidoglycan synthesis and the molecular targets of the penicillin antibiotics. Here, we report a combined crystallographic, small-angle X-ray scattering (SAXS) in-solution structure, computational and biophysical analysis of PBP1 of Staphylococcus aureus (saPBP1), providing mechanistic clues about its function and regulation during cell division. The structure reveals the pedestal domain, the transpeptidase domain, and most of the linker connecting to the "penicillin-binding protein and serine/threonine kinase associated" (PASTA) domains, but not its two PASTA domains, despite their presence in the construct. To address this absence, the structure of the PASTA domains was determined at 1.5 A resolution. Extensive molecular-dynamics simulations interpret the PASTA domains of saPBP1 as conformationally mobile and separated from the transpeptidase domain. This conclusion was confirmed by SAXS experiments on the full-length protein in solution. A series of crystallographic complexes with beta-lactam antibiotics (as inhibitors) and penta-Gly (as a substrate mimetic) allowed the molecular characterization of both inhibition by antibiotics and binding for the donor and acceptor peptidoglycan strands. Mass-spectrometry experiments with synthetic peptidoglycan fragments revealed binding by PASTA domains in coordination with the remaining domains. The observed mobility of the PASTA domain in saPBP1 could play a crucial role for in vivo interaction with its glycosyltransferase partner in the membrane or with other components of the divisome machinery, as well as for coordination of transpeptidation and polymerization processes in the bacterial divisome. | |||
Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus, an essential component of the divisome machinery.,Martinez-Caballero S, Mahasenan KV, Kim C, Molina R, Feltzer R, Lee M, Bouley R, Hesek D, Fisher JF, Munoz IG, Chang M, Mobashery S, Hermoso JA Comput Struct Biotechnol J. 2021 Sep 17;19:5392-5405. doi:, 10.1016/j.csbj.2021.09.018. eCollection 2021. PMID:34667534<ref>PMID:34667534</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7o4b" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Staphylococcus aureus subsp. aureus COL]] | |||
[[Category: Hermoso JA]] | [[Category: Hermoso JA]] | ||
[[Category: Martinez Caballero S]] | [[Category: Martinez Caballero S]] | ||
Revision as of 15:44, 1 February 2024
Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with penicillin GCrystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with penicillin G
Structural highlights
FunctionPublication Abstract from PubMedThe penicillin-binding proteins are the enzyme catalysts of the critical transpeptidation crosslinking polymerization reaction of bacterial peptidoglycan synthesis and the molecular targets of the penicillin antibiotics. Here, we report a combined crystallographic, small-angle X-ray scattering (SAXS) in-solution structure, computational and biophysical analysis of PBP1 of Staphylococcus aureus (saPBP1), providing mechanistic clues about its function and regulation during cell division. The structure reveals the pedestal domain, the transpeptidase domain, and most of the linker connecting to the "penicillin-binding protein and serine/threonine kinase associated" (PASTA) domains, but not its two PASTA domains, despite their presence in the construct. To address this absence, the structure of the PASTA domains was determined at 1.5 A resolution. Extensive molecular-dynamics simulations interpret the PASTA domains of saPBP1 as conformationally mobile and separated from the transpeptidase domain. This conclusion was confirmed by SAXS experiments on the full-length protein in solution. A series of crystallographic complexes with beta-lactam antibiotics (as inhibitors) and penta-Gly (as a substrate mimetic) allowed the molecular characterization of both inhibition by antibiotics and binding for the donor and acceptor peptidoglycan strands. Mass-spectrometry experiments with synthetic peptidoglycan fragments revealed binding by PASTA domains in coordination with the remaining domains. The observed mobility of the PASTA domain in saPBP1 could play a crucial role for in vivo interaction with its glycosyltransferase partner in the membrane or with other components of the divisome machinery, as well as for coordination of transpeptidation and polymerization processes in the bacterial divisome. Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus, an essential component of the divisome machinery.,Martinez-Caballero S, Mahasenan KV, Kim C, Molina R, Feltzer R, Lee M, Bouley R, Hesek D, Fisher JF, Munoz IG, Chang M, Mobashery S, Hermoso JA Comput Struct Biotechnol J. 2021 Sep 17;19:5392-5405. doi:, 10.1016/j.csbj.2021.09.018. eCollection 2021. PMID:34667534[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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