1tjl
From Proteopedia
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==Crystal structure of transcription factor DksA from E. coli== | ==Crystal structure of transcription factor DksA from E. coli== | ||
| - | <StructureSection load='1tjl' size='340' side='right' caption='[[1tjl]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='1tjl' size='340' side='right'caption='[[1tjl]], [[Resolution|resolution]] 2.00Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1tjl]] is a 10 chain structure with sequence from [ | + | <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> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id=' | + | <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> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <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> |
</table> | </table> | ||
== Function == | == 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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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]. | </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> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | 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. | ||
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| - | 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:15294156<ref>PMID:15294156</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1tjl" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Escherichia coli]] |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Artsimovitch I]] |
| - | [[Category: | + | [[Category: Perederina A]] |
| - | [[Category: Svetlov | + | [[Category: Svetlov V]] |
| - | [[Category: Vassylyev | + | [[Category: Vassylyev DG]] |
| - | [[Category: Vassylyeva | + | [[Category: Vassylyeva MN]] |
| - | [[Category: Yokoyama | + | [[Category: Yokoyama S]] |
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Current revision
Crystal structure of transcription factor DksA from E. coli
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