1pp5: Difference between revisions

Revision as of 07:15, 14 September 2022

Structure of Antibacterial Peptide Microcin J25: a 21-Residue Lariat Protoknot

Structural highlights

1pp5 is a 1 chain structure with sequence from Escherichia coli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	PRD_000184
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[MCJA_ECOLX] Peptide antibiotic that functions through inhibition of the bacterial DNA-dependent RNA polymerase (RNAP). May inhibit transcription by binding in RNAP secondary channel and blocking nucleotide substrates access to the catalytic center. Exhibits potent bacteriocidal activity against a range of Enterobacteriaceae, including several pathogenic E.coli, Salmonella and Shigella strains. Also acts on the cytoplasmic membrane of Salmonella newport, producing alteration of membrane permeability and disruption of the subsequent gradient dissipation, which inhibits several processes essential for cell viability, such as oxygen consumption. Induces bacterial filamentation in susceptible cells in a non-SOS-dependent way, but this phenotype may result from impaired transcription of genes coding for cell division proteins.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The antibacterial peptide microcin J25 (MccJ25) inhibits bacterial transcription by binding within, and obstructing, the nucleotide-uptake channel of bacterial RNA polymerase. Published covalent and three-dimensional structures indicate that MccJ25 is a 21-residue cycle. Here, we show that the published covalent and three-dimensional structures are incorrect, and that MccJ25 in fact is a 21-residue "lariat protoknot", consisting of an 8-residue cyclic segment followed by a 13-residue linear segment that loops back and threads through the cyclic segment. MccJ25 is the first example of a lariat protoknot involving a backbone-side chain amide linkage.

Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot.,Bayro MJ, Mukhopadhyay J, Swapna GV, Huang JY, Ma LC, Sineva E, Dawson PE, Montelione GT, Ebright RH J Am Chem Soc. 2003 Oct 15;125(41):12382-3. PMID:14531661^[4]

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

References

↑ Rintoul MR, de Arcuri BF, Salomon RA, Farias RN, Morero RD. The antibacterial action of microcin J25: evidence for disruption of cytoplasmic membrane energization in Salmonella newport. FEMS Microbiol Lett. 2001 Nov 13;204(2):265-70. PMID:11731133
↑ Delgado MA, Rintoul MR, Farias RN, Salomon RA. Escherichia coli RNA polymerase is the target of the cyclopeptide antibiotic microcin J25. J Bacteriol. 2001 Aug;183(15):4543-50. PMID:11443089 doi:https://dx.doi.org/10.1128/JB.183.15.4543-4550.2001
↑ Yuzenkova J, Delgado M, Nechaev S, Savalia D, Epshtein V, Artsimovitch I, Mooney RA, Landick R, Farias RN, Salomon R, Severinov K. Mutations of bacterial RNA polymerase leading to resistance to microcin j25. J Biol Chem. 2002 Dec 27;277(52):50867-75. Epub 2002 Oct 24. PMID:12401787 doi:https://dx.doi.org/10.1074/jbc.M209425200
↑ Bayro MJ, Mukhopadhyay J, Swapna GV, Huang JY, Ma LC, Sineva E, Dawson PE, Montelione GT, Ebright RH. Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot. J Am Chem Soc. 2003 Oct 15;125(41):12382-3. PMID:14531661 doi:10.1021/ja036677e

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Rintoul MR, de Arcuri BF, Salomon RA, Farias RN, Morero RD. The antibacterial action of microcin J25: evidence for disruption of cytoplasmic membrane energization in Salmonella newport. FEMS Microbiol Lett. 2001 Nov 13;204(2):265-70. PMID:11731133

[2] Delgado MA, Rintoul MR, Farias RN, Salomon RA. Escherichia coli RNA polymerase is the target of the cyclopeptide antibiotic microcin J25. J Bacteriol. 2001 Aug;183(15):4543-50. PMID:11443089 doi:https://dx.doi.org/10.1128/JB.183.15.4543-4550.2001

[3] Yuzenkova J, Delgado M, Nechaev S, Savalia D, Epshtein V, Artsimovitch I, Mooney RA, Landick R, Farias RN, Salomon R, Severinov K. Mutations of bacterial RNA polymerase leading to resistance to microcin j25. J Biol Chem. 2002 Dec 27;277(52):50867-75. Epub 2002 Oct 24. PMID:12401787 doi:https://dx.doi.org/10.1074/jbc.M209425200

[4] Bayro MJ, Mukhopadhyay J, Swapna GV, Huang JY, Ma LC, Sineva E, Dawson PE, Montelione GT, Ebright RH. Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot. J Am Chem Soc. 2003 Oct 15;125(41):12382-3. PMID:14531661 doi:10.1021/ja036677e

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==Structure of Antibacterial Peptide Microcin J25: a 21-Residue Lariat Protoknot==
-<StructureSection load='1pp5' size='340' side='right'caption='[[1pp5]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
+<StructureSection load='1pp5' size='340' side='right'caption='[[1pp5]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1pp5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PP5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PP5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1pp5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PP5 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MCJA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PRD_000184:Microcin+J25'>PRD_000184</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1pp5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pp5 OCA], [http://pdbe.org/1pp5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pp5 RCSB], [http://www.ebi.ac.uk/pdbsum/1pp5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pp5 ProSAT], [http://www.topsan.org/Proteins/NESGC/1pp5 TOPSAN]</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=1pp5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pp5 OCA], [https://pdbe.org/1pp5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pp5 RCSB], [https://www.ebi.ac.uk/pdbsum/1pp5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pp5 ProSAT], [https://www.topsan.org/Proteins/NESGC/1pp5 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MCJA_ECOLX MCJA_ECOLX]] Peptide antibiotic that functions through inhibition of the bacterial DNA-dependent RNA polymerase (RNAP). May inhibit transcription by binding in RNAP secondary channel and blocking nucleotide substrates access to the catalytic center. Exhibits potent bacteriocidal activity against a range of Enterobacteriaceae, including several pathogenic E.coli, Salmonella and Shigella strains. Also acts on the cytoplasmic membrane of Salmonella newport, producing alteration of membrane permeability and disruption of the subsequent gradient dissipation, which inhibits several processes essential for cell viability, such as oxygen consumption. Induces bacterial filamentation in susceptible cells in a non-SOS-dependent way, but this phenotype may result from impaired transcription of genes coding for cell division proteins.<ref>PMID:11731133</ref> <ref>PMID:11443089</ref> <ref>PMID:12401787</ref>
+[[https://www.uniprot.org/uniprot/MCJA_ECOLX MCJA_ECOLX]] Peptide antibiotic that functions through inhibition of the bacterial DNA-dependent RNA polymerase (RNAP). May inhibit transcription by binding in RNAP secondary channel and blocking nucleotide substrates access to the catalytic center. Exhibits potent bacteriocidal activity against a range of Enterobacteriaceae, including several pathogenic E.coli, Salmonella and Shigella strains. Also acts on the cytoplasmic membrane of Salmonella newport, producing alteration of membrane permeability and disruption of the subsequent gradient dissipation, which inhibits several processes essential for cell viability, such as oxygen consumption. Induces bacterial filamentation in susceptible cells in a non-SOS-dependent way, but this phenotype may result from impaired transcription of genes coding for cell division proteins.<ref>PMID:11731133</ref> <ref>PMID:11443089</ref> <ref>PMID:12401787</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Bayro, M J]]
+[[Category: Bayro MJ]]
-[[Category: Ebright, R H]]
+[[Category: Ebright RH]]
-[[Category: Huang, J Y]]
+[[Category: Huang JY]]
-[[Category: Ma, L C]]
+[[Category: Ma L-C]]
-[[Category: Montelione, G T]]
+[[Category: Montelione GT]]
-[[Category: Mukhopadhyay, J]]
+[[Category: Mukhopadhyay J]]
-[[Category: Structural genomic]]
+[[Category: Swapna GVT]]
-[[Category: Swapna, G V.T]]
-[[Category: Antibiotic]]
-[[Category: Backbone-sidechain amide linkage]]
-[[Category: Lariat]]
-[[Category: Nesg]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Protoknot]]

1pp5: Difference between revisions

Revision as of 07:15, 14 September 2022

Structure of Antibacterial Peptide Microcin J25: a 21-Residue Lariat Protoknot

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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