2c96: Difference between revisions

Latest revision as of 14:09, 13 December 2023

Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF

Structural highlights

2c96 is a 1 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.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	ATP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PSPF_ECOLI Transcriptional activator for the phage shock protein (psp) operon (pspABCDE) and pspG gene.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Bacterial enhancer-binding proteins (EBP) activate transcription by hydrolyzing ATP to restructure the sigma(54)-RNA polymerase-promoter complex. We compare six high resolution structures (<2.1 A) of the AAA(+) domain of EBP phage shock protein F (PspF) including apo, AMPPNP, Mg(2+)-ATP, and ADP forms. These structures permit a description of the atomic details underpinning the origins of the conformational changes occurring during ATP hydrolysis. Conserved regions of PspF's AAA(+) domain respond distinctively to nucleotide binding and hydrolysis, suggesting functional roles during the hydrolysis cycle, which completely agree with those derived from activities of PspF mutated at these positions. We propose a putative atomic switch that is responsible for coupling structural changes in the nucleotide-binding site to the repositioning of the sigma(54)-interacting loops. Striking similarities in nucleotide-specific conformational changes and atomic switch exist between PspF and the large T antigen helicase, suggesting conservation in the origin of those events amongst AAA(+) proteins.

Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF.,Rappas M, Schumacher J, Niwa H, Buck M, Zhang X J Mol Biol. 2006 Mar 24;357(2):481-92. Epub 2006 Jan 13. PMID:16430918^[4]

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

References

↑ Jovanovic G, Weiner L, Model P. Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. J Bacteriol. 1996 Apr;178(7):1936-45. PMID:8606168
↑ Lloyd LJ, Jones SE, Jovanovic G, Gyaneshwar P, Rolfe MD, Thompson A, Hinton JC, Buck M. Identification of a new member of the phage shock protein response in Escherichia coli, the phage shock protein G (PspG). J Biol Chem. 2004 Dec 31;279(53):55707-14. Epub 2004 Oct 13. PMID:15485810 doi:10.1074/jbc.M408994200
↑ Joly N, Burrows PC, Engl C, Jovanovic G, Buck M. A lower-order oligomer form of phage shock protein A (PspA) stably associates with the hexameric AAA(+) transcription activator protein PspF for negative regulation. J Mol Biol. 2009 Dec 11;394(4):764-75. doi: 10.1016/j.jmb.2009.09.055. Epub 2009 , Oct 3. PMID:19804784 doi:10.1016/j.jmb.2009.09.055
↑ Rappas M, Schumacher J, Niwa H, Buck M, Zhang X. Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF. J Mol Biol. 2006 Mar 24;357(2):481-92. Epub 2006 Jan 13. PMID:16430918 doi:10.1016/j.jmb.2005.12.052

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Jovanovic G, Weiner L, Model P. Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. J Bacteriol. 1996 Apr;178(7):1936-45. PMID:8606168

[2] Lloyd LJ, Jones SE, Jovanovic G, Gyaneshwar P, Rolfe MD, Thompson A, Hinton JC, Buck M. Identification of a new member of the phage shock protein response in Escherichia coli, the phage shock protein G (PspG). J Biol Chem. 2004 Dec 31;279(53):55707-14. Epub 2004 Oct 13. PMID:15485810 doi:10.1074/jbc.M408994200

[3] Joly N, Burrows PC, Engl C, Jovanovic G, Buck M. A lower-order oligomer form of phage shock protein A (PspA) stably associates with the hexameric AAA(+) transcription activator protein PspF for negative regulation. J Mol Biol. 2009 Dec 11;394(4):764-75. doi: 10.1016/j.jmb.2009.09.055. Epub 2009 , Oct 3. PMID:19804784 doi:10.1016/j.jmb.2009.09.055

[4] Rappas M, Schumacher J, Niwa H, Buck M, Zhang X. Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF. J Mol Biol. 2006 Mar 24;357(2):481-92. Epub 2006 Jan 13. PMID:16430918 doi:10.1016/j.jmb.2005.12.052

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF==
-<StructureSection load='2c96' size='340' side='right' caption='[[2c96]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='2c96' size='340' side='right'caption='[[2c96]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2c96]] is a 1 chain structure with sequence from [http://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=2C96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C96 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2c96]] is a 1 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=2C96 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C96 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2bjv|2bjv]], [[2bjw|2bjw]], [[2c98|2c98]], [[2c99|2c99]], [[2c9c|2c9c]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></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=2c96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c96 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c96 RCSB], [http://www.ebi.ac.uk/pdbsum/2c96 PDBsum]</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=2c96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c96 OCA], [https://pdbe.org/2c96 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c96 RCSB], [https://www.ebi.ac.uk/pdbsum/2c96 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c96 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PSPF_ECOLI PSPF_ECOLI]] Transcriptional activator for the phage shock protein (psp) operon (pspABCDE) and pspG gene.<ref>PMID:8606168</ref> <ref>PMID:15485810</ref> <ref>PMID:19804784</ref>
+[https://www.uniprot.org/uniprot/PSPF_ECOLI PSPF_ECOLI] Transcriptional activator for the phage shock protein (psp) operon (pspABCDE) and pspG gene.<ref>PMID:8606168</ref> <ref>PMID:15485810</ref> <ref>PMID:19804784</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c9/2c96_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c9/2c96_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2c96 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2c96" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Transcriptional activator|Transcriptional activator]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli k-12]]
+[[Category: Escherichia coli K-12]]
-[[Category: Buck, M]]
+[[Category: Large Structures]]
-[[Category: Niwa, H]]
+[[Category: Buck M]]
-[[Category: Rappas, M]]
+[[Category: Niwa H]]
-[[Category: Schumacher, J]]
+[[Category: Rappas M]]
-[[Category: Zhang, X]]
+[[Category: Schumacher J]]
-[[Category: Aaa domain]]
+[[Category: Zhang X]]
-[[Category: Activator]]
-[[Category: Atp-binding]]
-[[Category: Atpase]]
-[[Category: Bacterial sigma54 activator]]
-[[Category: Dna-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: Sensory transduction]]
-[[Category: Transcription regulation]]
-[[Category: Two-component regulatory system]]

2c96: Difference between revisions

Latest revision as of 14:09, 13 December 2023

Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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