7onw: Difference between revisions

Revision as of 12:53, 1 February 2024

Crystal structure of PBP3 from E. coli in complex with AIC499

Structural highlights

7onw is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	MPD, PO4, VL5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FTSI_ECOLI Essential cell division protein that catalyzes cross-linking of the peptidoglycan cell wall at the division septum (PubMed:1103132, PubMed:6450748, PubMed:9614966, PubMed:3531167, PubMed:7030331). Required for localization of FtsN (PubMed:9282742).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

Novel antimicrobial strategies are urgently required because of the rising threat of multi drug resistant bacterial strains and the infections caused by them. Among the available target structures, the so-called penicillin binding proteins are of particular interest, owing to their good accessibility in the periplasmic space, and the lack of homologous proteins in humans, reducing the risk of side effects of potential drugs. In this report, we focus on the interaction of the innovative beta-lactam antibiotic AIC499 with penicillin binding protein 3 (PBP3) from Escherichia coli and Pseudomonas aeruginosa. This recently developed monobactam displays broad antimicrobial activity, against Gram-negative strains, and improved resistance to most classes of beta-lactamases. By analyzing crystal structures of the respective complexes, we were able to explore the binding mode of AIC499 to its target proteins. In addition, the apo structures determined for PBP3, from P. aeruginosa and the catalytic transpeptidase domain of the E. coli orthologue, provide new insights into the dynamics of these proteins and the impact of drug binding.

Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria.,Freischem S, Grimm I, Lopez-Perez A, Willbold D, Klenke B, Vuong C, Dingley AJ, Weiergraber OH Biomolecules. 2021 Jul 19;11(7). pii: biom11071057. doi: 10.3390/biom11071057. PMID:34356681^[7]

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

References

↑ Spratt BG. Distinct penicillin binding proteins involved in the division, elongation, and shape of Escherichia coli K12. Proc Natl Acad Sci U S A. 1975 Aug;72(8):2999-3003. PMID:1103132
↑ Pisabarro AG, Prats R, Vaquez D, Rodriguez-Tebar A. Activity of penicillin-binding protein 3 from Escherichia coli. J Bacteriol. 1986 Oct;168(1):199-206. doi: 10.1128/jb.168.1.199-206.1986. PMID:3531167 doi:https://dx.doi.org/10.1128/jb.168.1.199-206.1986
↑ Botta GA, Park JT. Evidence for involvement of penicillin-binding protein 3 in murein synthesis during septation but not during cell elongation. J Bacteriol. 1981 Jan;145(1):333-40. doi: 10.1128/jb.145.1.333-340.1981. PMID:6450748 doi:https://dx.doi.org/10.1128/jb.145.1.333-340.1981
↑ Ishino F, Matsuhashi M. Peptidoglycan synthetic enzyme activities of highly purified penicillin-binding protein 3 in Escherichia coli: a septum-forming reaction sequence. Biochem Biophys Res Commun. 1981 Aug 14;101(3):905-11. doi:, 10.1016/0006-291x(81)91835-0. PMID:7030331 doi:https://dx.doi.org/10.1016/0006-291x(81)91835-0
↑ Addinall SG, Cao C, Lutkenhaus J. FtsN, a late recruit to the septum in Escherichia coli. Mol Microbiol. 1997 Jul;25(2):303-9. doi: 10.1046/j.1365-2958.1997.4641833.x. PMID:9282742 doi:https://dx.doi.org/10.1046/j.1365-2958.1997.4641833.x
↑ Nguyen-Disteche M, Fraipont C, Buddelmeijer N, Nanninga N. The structure and function of Escherichia coli penicillin-binding protein 3. Cell Mol Life Sci. 1998 Apr;54(4):309-16. doi: 10.1007/s000180050157. PMID:9614966 doi:https://dx.doi.org/10.1007/s000180050157
↑ Freischem S, Grimm I, Lopez-Perez A, Willbold D, Klenke B, Vuong C, Dingley AJ, Weiergraber OH. Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria. Biomolecules. 2021 Jul 19;11(7). pii: biom11071057. doi: 10.3390/biom11071057. PMID:34356681 doi:https://dx.doi.org/10.3390/biom11071057

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OCA

[1] Spratt BG. Distinct penicillin binding proteins involved in the division, elongation, and shape of Escherichia coli K12. Proc Natl Acad Sci U S A. 1975 Aug;72(8):2999-3003. PMID:1103132

[2] Pisabarro AG, Prats R, Vaquez D, Rodriguez-Tebar A. Activity of penicillin-binding protein 3 from Escherichia coli. J Bacteriol. 1986 Oct;168(1):199-206. doi: 10.1128/jb.168.1.199-206.1986. PMID:3531167 doi:https://dx.doi.org/10.1128/jb.168.1.199-206.1986

[3] Botta GA, Park JT. Evidence for involvement of penicillin-binding protein 3 in murein synthesis during septation but not during cell elongation. J Bacteriol. 1981 Jan;145(1):333-40. doi: 10.1128/jb.145.1.333-340.1981. PMID:6450748 doi:https://dx.doi.org/10.1128/jb.145.1.333-340.1981

[4] Ishino F, Matsuhashi M. Peptidoglycan synthetic enzyme activities of highly purified penicillin-binding protein 3 in Escherichia coli: a septum-forming reaction sequence. Biochem Biophys Res Commun. 1981 Aug 14;101(3):905-11. doi:, 10.1016/0006-291x(81)91835-0. PMID:7030331 doi:https://dx.doi.org/10.1016/0006-291x(81)91835-0

[5] Addinall SG, Cao C, Lutkenhaus J. FtsN, a late recruit to the septum in Escherichia coli. Mol Microbiol. 1997 Jul;25(2):303-9. doi: 10.1046/j.1365-2958.1997.4641833.x. PMID:9282742 doi:https://dx.doi.org/10.1046/j.1365-2958.1997.4641833.x

[6] Nguyen-Disteche M, Fraipont C, Buddelmeijer N, Nanninga N. The structure and function of Escherichia coli penicillin-binding protein 3. Cell Mol Life Sci. 1998 Apr;54(4):309-16. doi: 10.1007/s000180050157. PMID:9614966 doi:https://dx.doi.org/10.1007/s000180050157

[7] Freischem S, Grimm I, Lopez-Perez A, Willbold D, Klenke B, Vuong C, Dingley AJ, Weiergraber OH. Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria. Biomolecules. 2021 Jul 19;11(7). pii: biom11071057. doi: 10.3390/biom11071057. PMID:34356681 doi:https://dx.doi.org/10.3390/biom11071057

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[2]

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[5]

[6]

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@@ Line 3: / Line 3: @@
 <StructureSection load='7onw' size='340' side='right'caption='[[7onw]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7onw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ONW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ONW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7onw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ONW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ONW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=VL5:(2S)-2-[(Z)-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2S)-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[N-[(3R)-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic+acid'>VL5</scene></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]] 2.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7onn|7onn]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=VL5:(2S)-2-[(Z)-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2S)-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[N-[(3R)-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic+acid'>VL5</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ftsI, pbpB, b0084, JW0082 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=7onw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7onw OCA], [https://pdbe.org/7onw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7onw RCSB], [https://www.ebi.ac.uk/pdbsum/7onw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7onw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/FTSI_ECOLI FTSI_ECOLI]] Essential cell division protein that catalyzes cross-linking of the peptidoglycan cell wall at the division septum (PubMed:1103132, PubMed:6450748, PubMed:9614966, PubMed:3531167, PubMed:7030331). Required for localization of FtsN (PubMed:9282742).<ref>PMID:1103132</ref> <ref>PMID:3531167</ref> <ref>PMID:6450748</ref> <ref>PMID:7030331</ref> <ref>PMID:9282742</ref> <ref>PMID:9614966</ref>
+[https://www.uniprot.org/uniprot/FTSI_ECOLI FTSI_ECOLI] Essential cell division protein that catalyzes cross-linking of the peptidoglycan cell wall at the division septum (PubMed:1103132, PubMed:6450748, PubMed:9614966, PubMed:3531167, PubMed:7030331). Required for localization of FtsN (PubMed:9282742).<ref>PMID:1103132</ref> <ref>PMID:3531167</ref> <ref>PMID:6450748</ref> <ref>PMID:7030331</ref> <ref>PMID:9282742</ref> <ref>PMID:9614966</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 19: @@
 </div>
 <div class="pdbe-citations 7onw" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
+[[Category: Freischem S]]
-[[Category: Freischem, S]]
+[[Category: Grimm I]]
-[[Category: Grimm, I]]
+[[Category: Weiergraeber OH]]
-[[Category: Weiergraeber, O H]]
-[[Category: Drug complex]]
-[[Category: Monobactam]]
-[[Category: Pbp3]]
-[[Category: Peptidoglycan synthesis]]
-[[Category: Protein binding]]

7onw: Difference between revisions

Revision as of 12:53, 1 February 2024

Crystal structure of PBP3 from E. coli in complex with AIC499

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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