|
|
| (4 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | [[Image:3qoq.png|left|200px]] | |
| | | | |
| - | <!-- | + | ==Crystal Structure of the Transcription Factor AmrZ in Complex with the 18 Base Pair amrZ1 Binding Site== |
| - | The line below this paragraph, containing "STRUCTURE_3qoq", creates the "Structure Box" on the page.
| + | <StructureSection load='3qoq' size='340' side='right'caption='[[3qoq]], [[Resolution|resolution]] 3.10Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[3qoq]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QOQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QOQ FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> |
| - | --> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | {{STRUCTURE_3qoq| PDB=3qoq | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3qoq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qoq OCA], [https://pdbe.org/3qoq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qoq RCSB], [https://www.ebi.ac.uk/pdbsum/3qoq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qoq ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/AMRZ_PSEAE AMRZ_PSEAE] Functions both as a transcriptional activator and a repressor of multiple genes encoding virulence factors as well as genes involved in environmental adaptation (PubMed:16352829, PubMed:22511872, PubMed:26549743). Plays a role in alginate production via the activation of AlgD which is the first gene in the alginate biosynthetic operon (PubMed:10476040, PubMed:16352829). Regulates also the transcription of genes responsible for type IV pili localization and twitching motility (PubMed:16352829). Mediates transition of P.aeruginosa biofilm infections from colonizing to chronic biofilms through repression of the psl operon (PubMed:23354748). Represses also its own transcription by binding to two sites on amrZ promoter, amrZ1 and amrZ2 (PubMed:15968052).<ref>PMID:10476040</ref> <ref>PMID:15968052</ref> <ref>PMID:16352829</ref> <ref>PMID:22511872</ref> <ref>PMID:23354748</ref> <ref>PMID:26549743</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | AmrZ, a member of the Ribbon-Helix-Helix family of DNA binding proteins, functions as both a transcriptional activator and repressor of multiple genes encoding Pseudomonas aeruginosa virulence factors. The expression of these virulence factors leads to chronic and sustained infections associated with worsening prognosis. In this study, we present the X-ray crystal structure of AmrZ in complex with DNA containing the repressor site, amrZ1. Binding of AmrZ to this site leads to auto-repression. AmrZ binds this DNA sequence as a dimer-of-dimers, and makes specific base contacts to two half sites, separated by a five base pair linker region. Analysis of the linker region shows a narrowing of the minor groove, causing significant distortions. AmrZ binding assays utilizing sequences containing variations in this linker region reveals that secondary structure of the DNA, conferred by the sequence of this region, is an important determinant in binding affinity. The results from these experiments allow for the creation of a model where both intrinsic structure of the DNA and specific nucleotide recognition are absolutely necessary for binding of the protein. We also examined AmrZ binding to the algD promoter, which results in activation of the alginate exopolysaccharide biosynthetic operon, and found the protein utilizes different interactions with this site. Finally, we tested the in vivo effects of this differential binding by switching the AmrZ binding site at algD, where it acts as an activator, for a repressor binding sequence and show that differences in binding alone do not affect transcriptional regulation. |
| | | | |
| - | ===Crystal Structure of the Transcription Factor AmrZ in Complex with the 18 Base Pair amrZ1 Binding Site===
| + | The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes.,Pryor EE Jr, Waligora EA, Xu B, Dellos-Nolan S, Wozniak DJ, Hollis T PLoS Pathog. 2012 Apr;8(4):e1002648. Epub 2012 Apr 12. PMID:22511872<ref>PMID:22511872</ref> |
| | | | |
| - | | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | <!--
| + | </div> |
| - | The line below this paragraph, {{ABSTRACT_PUBMED_22511872}}, adds the Publication Abstract to the page
| + | <div class="pdbe-citations 3qoq" style="background-color:#fffaf0;"></div> |
| - | (as it appears on PubMed at http://www.pubmed.gov), where 22511872 is the PubMed ID number.
| + | == References == |
| - | -->
| + | <references/> |
| - | {{ABSTRACT_PUBMED_22511872}}
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==About this Structure== | + | [[Category: Large Structures]] |
| - | [[3qoq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QOQ OCA].
| + | |
| - | | + | |
| - | ==Reference== | + | |
| - | <ref group="xtra">PMID:022511872</ref><references group="xtra"/> | + | |
| | [[Category: Pseudomonas aeruginosa]] | | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Hollis, T.]] | + | [[Category: Hollis T]] |
| - | [[Category: Pryor,, E E.]] | + | [[Category: Pryor Jr EE]] |
| - | [[Category: Wozniak, D J.]] | + | [[Category: Wozniak DJ]] |
| - | [[Category: Dna binding]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Ribbon-helix-helix]]
| + | |
| - | [[Category: Transcription factor]]
| + | |
| - | [[Category: Transcription-dna complex]]
| + | |
| Structural highlights
Function
AMRZ_PSEAE Functions both as a transcriptional activator and a repressor of multiple genes encoding virulence factors as well as genes involved in environmental adaptation (PubMed:16352829, PubMed:22511872, PubMed:26549743). Plays a role in alginate production via the activation of AlgD which is the first gene in the alginate biosynthetic operon (PubMed:10476040, PubMed:16352829). Regulates also the transcription of genes responsible for type IV pili localization and twitching motility (PubMed:16352829). Mediates transition of P.aeruginosa biofilm infections from colonizing to chronic biofilms through repression of the psl operon (PubMed:23354748). Represses also its own transcription by binding to two sites on amrZ promoter, amrZ1 and amrZ2 (PubMed:15968052).[1] [2] [3] [4] [5] [6]
Publication Abstract from PubMed
AmrZ, a member of the Ribbon-Helix-Helix family of DNA binding proteins, functions as both a transcriptional activator and repressor of multiple genes encoding Pseudomonas aeruginosa virulence factors. The expression of these virulence factors leads to chronic and sustained infections associated with worsening prognosis. In this study, we present the X-ray crystal structure of AmrZ in complex with DNA containing the repressor site, amrZ1. Binding of AmrZ to this site leads to auto-repression. AmrZ binds this DNA sequence as a dimer-of-dimers, and makes specific base contacts to two half sites, separated by a five base pair linker region. Analysis of the linker region shows a narrowing of the minor groove, causing significant distortions. AmrZ binding assays utilizing sequences containing variations in this linker region reveals that secondary structure of the DNA, conferred by the sequence of this region, is an important determinant in binding affinity. The results from these experiments allow for the creation of a model where both intrinsic structure of the DNA and specific nucleotide recognition are absolutely necessary for binding of the protein. We also examined AmrZ binding to the algD promoter, which results in activation of the alginate exopolysaccharide biosynthetic operon, and found the protein utilizes different interactions with this site. Finally, we tested the in vivo effects of this differential binding by switching the AmrZ binding site at algD, where it acts as an activator, for a repressor binding sequence and show that differences in binding alone do not affect transcriptional regulation.
The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes.,Pryor EE Jr, Waligora EA, Xu B, Dellos-Nolan S, Wozniak DJ, Hollis T PLoS Pathog. 2012 Apr;8(4):e1002648. Epub 2012 Apr 12. PMID:22511872[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Baynham PJ, Brown AL, Hall LL, Wozniak DJ. Pseudomonas aeruginosa AlgZ, a ribbon-helix-helix DNA-binding protein, is essential for alginate synthesis and algD transcriptional activation. Mol Microbiol. 1999 Sep;33(5):1069-80. PMID:10476040 doi:10.1046/j.1365-2958.1999.01550.x
- ↑ Ramsey DM, Baynham PJ, Wozniak DJ. Binding of Pseudomonas aeruginosa AlgZ to sites upstream of the algZ promoter leads to repression of transcription. J Bacteriol. 2005 Jul;187(13):4430-43. PMID:15968052 doi:10.1128/JB.187.13.4430-4443.2005
- ↑ Baynham PJ, Ramsey DM, Gvozdyev BV, Cordonnier EM, Wozniak DJ. The Pseudomonas aeruginosa ribbon-helix-helix DNA-binding protein AlgZ (AmrZ) controls twitching motility and biogenesis of type IV pili. J Bacteriol. 2006 Jan;188(1):132-40. PMID:16352829 doi:10.1128/JB.188.1.132-140.2006
- ↑ Pryor EE Jr, Waligora EA, Xu B, Dellos-Nolan S, Wozniak DJ, Hollis T. The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes. PLoS Pathog. 2012 Apr;8(4):e1002648. Epub 2012 Apr 12. PMID:22511872 doi:10.1371/journal.ppat.1002648
- ↑ Jones CJ, Ryder CR, Mann EE, Wozniak DJ. AmrZ modulates Pseudomonas aeruginosa biofilm architecture by directly repressing transcription of the psl operon. J Bacteriol. 2013 Apr;195(8):1637-44. PMID:23354748 doi:10.1128/JB.02190-12
- ↑ Xu B, Ju Y, Soukup RJ, Ramsey DM, Fishel R, Wysocki VH, Wozniak DJ. The Pseudomonas aeruginosa AmrZ C-terminal domain mediates tetramerization and is required for its activator and repressor functions. Environ Microbiol Rep. 2016 Feb;8(1):85-90. PMID:26549743 doi:10.1111/1758-2229.12354
- ↑ Pryor EE Jr, Waligora EA, Xu B, Dellos-Nolan S, Wozniak DJ, Hollis T. The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes. PLoS Pathog. 2012 Apr;8(4):e1002648. Epub 2012 Apr 12. PMID:22511872 doi:10.1371/journal.ppat.1002648
|
