3qoq

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of the Transcription Factor AmrZ in Complex with the 18 Base Pair amrZ1 Binding Site

Structural highlights

3qoq is a 6 chain structure with sequence from Pseudomonas aeruginosa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.1Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

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/3qoq"

Categories: Large Structures | Pseudomonas aeruginosa | Hollis T | Pryor Jr EE | Wozniak DJ

@@ Line 3: / Line 3: @@
 <StructureSection load='3qoq' size='340' side='right'caption='[[3qoq]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3qoq]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. 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>
+<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>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 3.1&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">algZ, amrZ, PA3385 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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>
 <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 ==
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Hollis, T]]
+[[Category: Pseudomonas aeruginosa]]
-[[Category: Pryor, E E]]
+[[Category: Hollis T]]
-[[Category: Wozniak, D J]]
+[[Category: Pryor Jr EE]]
-[[Category: Dna binding]]
+[[Category: Wozniak DJ]]
-[[Category: Protein-dna complex]]
-[[Category: Ribbon-helix-helix]]
-[[Category: Transcription factor]]
-[[Category: Transcription-dna complex]]

3qoq

From Proteopedia

Current revision

Crystal Structure of the Transcription Factor AmrZ in Complex with the 18 Base Pair amrZ1 Binding Site

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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