7onn

From Proteopedia

(Difference between revisions)

Revision as of 07:04, 22 September 2021

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

Structural highlights

7onn is a 1 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	7onk
Gene:	ftsI, pbpB, b0084, JW0082 (ECOLI)
Activity:	Serine-type D-Ala-D-Ala carboxypeptidase, with EC number 3.4.16.4
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:http://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:http://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:http://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:http://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:http://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:http://dx.doi.org/10.3390/biom11071057

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/7onn"

@@ Line 1: / Line 1: @@
 ==Crystal structure of PBP3 transpeptidase domain from E. coli in complex with AIC499==
-<StructureSection load='7onn' size='340' side='right'caption='[[7onn]]' scene=''>
+<StructureSection load='7onn' size='340' side='right'caption='[[7onn]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ONN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ONN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7onn]] 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=7ONN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ONN 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=7onn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7onn OCA], [https://pdbe.org/7onn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7onn RCSB], [https://www.ebi.ac.uk/pdbsum/7onn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7onn ProSAT]</span></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=12P:DODECAETHYLENE+GLYCOL'>12P</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7onk|7onk]]</div></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=7onn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7onn OCA], [https://pdbe.org/7onn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7onn RCSB], [https://www.ebi.ac.uk/pdbsum/7onn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7onn 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>
+<div style="background-color:#fffaf0;">
+== 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<ref>PMID:34356681</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 7onn" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
+[[Category: Ecoli]]
 [[Category: Large Structures]]
-[[Category: Freischem S]]
+[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-[[Category: Grimm I]]
+[[Category: Freischem, S]]
-[[Category: Weiergraeber OH]]
+[[Category: Grimm, I]]
+[[Category: Weiergraeber, O H]]
+[[Category: Drug complex]]
+[[Category: Monobactam]]
+[[Category: Pbp3]]
+[[Category: Peptidoglycan synthesis]]
+[[Category: Protein binding]]
+[[Category: Transpeptidase domain]]

7onn

From Proteopedia

Revision as of 07:04, 22 September 2021

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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