1tjl: Difference between revisions

Latest revision as of 13:30, 13 March 2024

Crystal structure of transcription factor DksA from E. coli

Structural highlights

1tjl is a 10 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

DKSA_ECOLI Transcription factor that acts by binding directly to the RNA polymerase (RNAP). Required for negative regulation of rRNA expression and positive regulation of several amino acid biosynthesis promoters. Also required for regulation of fis expression. Binding to RNAP disrupts interaction of RNAP with DNA, inhibits formation of initiation complexes, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription. Inhibits transcript elongation, exonucleolytic RNA cleavage and pyrophosphorolysis, and increases intrinsic termination. Also involved, with RecN, in repair of DNA double-strand breaks.^[1] ^[2] ^[3] ^[4] ^[5]

Evolutionary Conservation

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

References

↑ Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, Foster JW, Gourse RL. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell. 2004 Aug 6;118(3):311-22. PMID:15294157 doi:https://dx.doi.org/10.1016/j.cell.2004.07.009
↑ Meddows TR, Savory AP, Grove JI, Moore T, Lloyd RG. RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double-strand breaks. Mol Microbiol. 2005 Jul;57(1):97-110. PMID:15948952 doi:https://dx.doi.org/10.1111/j.1365-2958.2005.04677.x
↑ Mallik P, Paul BJ, Rutherford ST, Gourse RL, Osuna R. DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J Bacteriol. 2006 Aug;188(16):5775-82. PMID:16885445 doi:https://dx.doi.org/10.1128/JB.00276-06
↑ Furman R, Sevostyanova A, Artsimovitch I. Transcription initiation factor DksA has diverse effects on RNA chain elongation. Nucleic Acids Res. 2012 Apr;40(8):3392-402. doi: 10.1093/nar/gkr1273. Epub 2011, Dec 30. PMID:22210857 doi:https://dx.doi.org/10.1093/nar/gkr1273
↑ Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell. 2004 Aug 6;118(3):297-309. PMID:15294156 doi:10.1016/j.cell.2004.06.030

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OCA

[1] Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, Foster JW, Gourse RL. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell. 2004 Aug 6;118(3):311-22. PMID:15294157 doi:https://dx.doi.org/10.1016/j.cell.2004.07.009

[2] Meddows TR, Savory AP, Grove JI, Moore T, Lloyd RG. RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double-strand breaks. Mol Microbiol. 2005 Jul;57(1):97-110. PMID:15948952 doi:https://dx.doi.org/10.1111/j.1365-2958.2005.04677.x

[3] Mallik P, Paul BJ, Rutherford ST, Gourse RL, Osuna R. DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J Bacteriol. 2006 Aug;188(16):5775-82. PMID:16885445 doi:https://dx.doi.org/10.1128/JB.00276-06

[4] Furman R, Sevostyanova A, Artsimovitch I. Transcription initiation factor DksA has diverse effects on RNA chain elongation. Nucleic Acids Res. 2012 Apr;40(8):3392-402. doi: 10.1093/nar/gkr1273. Epub 2011, Dec 30. PMID:22210857 doi:https://dx.doi.org/10.1093/nar/gkr1273

[5] Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell. 2004 Aug 6;118(3):297-309. PMID:15294156 doi:10.1016/j.cell.2004.06.030

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[5]

@@ Line 1: / Line 1: @@
-[[Image:1tjl.gif|left|200px]]<br /><applet load="1tjl" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1tjl, resolution 2.00&Aring;" />
-'''Crystal structure of transcription factor DksA from E. coli'''<br />
-==Overview==
+==Crystal structure of transcription factor DksA from E. coli==
-Bacterial transcription is regulated by the alarmone ppGpp, which binds, near the catalytic site of RNA polymerase (RNAP) and modulates its, activity. We show that the DksA protein is a crucial component of, ppGpp-dependent regulation. The 2.0 A resolution structure of Escherichia, coli DksA reveals a globular domain and a coiled coil with two highly, conserved Asp residues at its tip that is reminiscent of the transcript, cleavage factor GreA. This structural similarity suggests that DksA coiled, coil protrudes into the RNAP secondary channel to coordinate a ppGpp bound, Mg2+ ion with the Asp residues, thereby stabilizing the ppGpp-RNAP, complex. Biochemical analysis demonstrates that DksA affects transcript, elongation, albeit differently from GreA; augments ppGpp effects on, initiation; and binds directly to RNAP, positioning the Asp residues near, the active site. Substitution of these residues eliminates the synergy, between DksA and ppGpp. Thus, the secondary channel emerges as a common, regulatory entrance for transcription factors.
+<StructureSection load='1tjl' size='340' side='right'caption='[[1tjl]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1tjl]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TJL FirstGlance]. <br>
-TJL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TJL OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tjl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tjl OCA], [https://pdbe.org/1tjl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tjl RCSB], [https://www.ebi.ac.uk/pdbsum/1tjl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tjl ProSAT], [https://www.topsan.org/Proteins/RSGI/1tjl TOPSAN]</span></td></tr>
-Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription., Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG, Cell. 2004 Aug 6;118(3):297-309. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15294156 15294156]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DKSA_ECOLI DKSA_ECOLI] Transcription factor that acts by binding directly to the RNA polymerase (RNAP). Required for negative regulation of rRNA expression and positive regulation of several amino acid biosynthesis promoters. Also required for regulation of fis expression. Binding to RNAP disrupts interaction of RNAP with DNA, inhibits formation of initiation complexes, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription. Inhibits transcript elongation, exonucleolytic RNA cleavage and pyrophosphorolysis, and increases intrinsic termination. Also involved, with RecN, in repair of DNA double-strand breaks.<ref>PMID:15294157</ref> <ref>PMID:15948952</ref> <ref>PMID:16885445</ref> <ref>PMID:22210857</ref> <ref>PMID:15294156</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/tj/1tjl_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/main_output.php?pdb_ID=1tjl ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Artsimovitch, I.]]
+[[Category: Artsimovitch I]]
-[[Category: Perederina, A.]]
+[[Category: Perederina A]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+[[Category: Svetlov V]]
-[[Category: Svetlov, V.]]
+[[Category: Vassylyev DG]]
-[[Category: Vassylyev, D.G.]]
+[[Category: Vassylyeva MN]]
-[[Category: Vassylyeva, M.N.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
-[[Category: ZN]]
-[[Category: dksa]]
-[[Category: ppgpp]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rna polymerase]]
-[[Category: rsgi]]
-[[Category: stringent response]]
-[[Category: structural genomics]]
-[[Category: transcription factor]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:19:28 2007''

1tjl: Difference between revisions

Latest revision as of 13:30, 13 March 2024

Crystal structure of transcription factor DksA from E. coli

Structural highlights

Function

Evolutionary Conservation

References

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