4gcs: Difference between revisions

Revision as of 06:48, 26 October 2022

Crystal Structure of E. coli OmpF porin in complex with Ertapenem

Structural highlights

4gcs is a 2 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.
Ligands:	1RG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OMPF_ECOLI Forms pores that allow passive diffusion of small molecules across the outer membrane. It is also a receptor for the bacteriophage T2.^[1]

Publication Abstract from PubMed

The structure of OmpF porin in complex with three common antibiotics (zwitterionic ampicillin, anionic ertapenem, and di-anionic carbenicillin) was determined using X-ray crystallography. The three antibiotics are found to bind within the extracellular and periplasmic pore vestibules, away from the narrow OmpF constriction zone. Using the X-ray structures as a starting point, nonequilibrium molecular dynamics simulations with an applied membrane voltage show that ionic current through the OmpF channel is blocked with bound ampicillin, but not with bound carbenicillin. The susceptibility of Escherichia coli expressing OmpF mutants to ampicillin and carbenicillin was also experimentally characterized using microbiologic assays. These results show that general diffusion by OmpF porins allows for transfer of molecules with varied charged states and give insights into the design of more efficient antibiotics. A better understanding of this mechanism will shed light on nature's way of devising channels able to enhance the transport of molecules through membranes.

The Binding of Antibiotics in OmpF Porin.,Ziervogel BK, Roux B Structure. 2012 Nov 27. pii: S0969-2126(12)00410-8. doi:, 10.1016/j.str.2012.10.014. PMID:23201272^[2]

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

References

↑ Duval V, Nicoloff H, Levy SB. Combined inactivation of lon and ycgE decreases multidrug susceptibility by reducing the amount of OmpF porin in Escherichia coli. Antimicrob Agents Chemother. 2009 Nov;53(11):4944-8. doi: 10.1128/AAC.00787-09., Epub 2009 Aug 31. PMID:19721064 doi:10.1128/AAC.00787-09
↑ Ziervogel BK, Roux B. The Binding of Antibiotics in OmpF Porin. Structure. 2012 Nov 27. pii: S0969-2126(12)00410-8. doi:, 10.1016/j.str.2012.10.014. PMID:23201272 doi:https://dx.doi.org/10.1016/j.str.2012.10.014

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OCA

[1] Duval V, Nicoloff H, Levy SB. Combined inactivation of lon and ycgE decreases multidrug susceptibility by reducing the amount of OmpF porin in Escherichia coli. Antimicrob Agents Chemother. 2009 Nov;53(11):4944-8. doi: 10.1128/AAC.00787-09., Epub 2009 Aug 31. PMID:19721064 doi:10.1128/AAC.00787-09

[2] Ziervogel BK, Roux B. The Binding of Antibiotics in OmpF Porin. Structure. 2012 Nov 27. pii: S0969-2126(12)00410-8. doi:, 10.1016/j.str.2012.10.014. PMID:23201272 doi:https://dx.doi.org/10.1016/j.str.2012.10.014

[1]

[2]

@@ Line 1: / Line 1: @@
 ==Crystal Structure of E. coli OmpF porin in complex with Ertapenem==
-<StructureSection load='4gcs' size='340' side='right' caption='[[4gcs]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
+<StructureSection load='4gcs' size='340' side='right'caption='[[4gcs]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4gcs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GCS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4gcs]] is a 2 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=4GCS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GCS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1RG:(4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL)CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC+ACID'>1RG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1RG:(4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL)CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC+ACID'>1RG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gcp|4gcp]], [[4gcq|4gcq]]</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=4gcs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcs OCA], [https://pdbe.org/4gcs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gcs RCSB], [https://www.ebi.ac.uk/pdbsum/4gcs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gcs ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ompF, cmlB, coa, cry, tolF, b0929, JW0912 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gcs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcs OCA], [http://pdbe.org/4gcs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gcs RCSB], [http://www.ebi.ac.uk/pdbsum/4gcs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gcs ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/OMPF_ECOLI OMPF_ECOLI]] Forms pores that allow passive diffusion of small molecules across the outer membrane. It is also a receptor for the bacteriophage T2.<ref>PMID:19721064</ref>
+[https://www.uniprot.org/uniprot/OMPF_ECOLI OMPF_ECOLI] Forms pores that allow passive diffusion of small molecules across the outer membrane. It is also a receptor for the bacteriophage T2.<ref>PMID:19721064</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 20: @@
 ==See Also==
-*[[Porin|Porin]]
+*[[Porin 3D structures|Porin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Roux, B]]
+[[Category: Large Structures]]
-[[Category: Ziervogel, B K]]
+[[Category: Roux B]]
-[[Category: Beta-barrel]]
+[[Category: Ziervogel BK]]
-[[Category: Ertapenem binding]]
-[[Category: Membrane protein-antibiotic complex]]
-[[Category: Non-specific channel]]
-[[Category: Outer membrane]]
-[[Category: Protein-drug complex]]
-[[Category: Trimer]]

4gcs: Difference between revisions

Revision as of 06:48, 26 October 2022

Crystal Structure of E. coli OmpF porin in complex with Ertapenem

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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