This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1tjl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:30, 13 March 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1tjl.png|left|200px]]
 
-
<!--
+
==Crystal structure of transcription factor DksA from E. coli==
-
The line below this paragraph, containing "STRUCTURE_1tjl", creates the "Structure Box" on the page.
+
<StructureSection load='1tjl' size='340' side='right'caption='[[1tjl]], [[Resolution|resolution]] 2.00&Aring;' 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'>[[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>
-
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]] 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>
-
{{STRUCTURE_1tjl| PDB=1tjl | SCENE= }}
+
<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>
-
===Crystal structure of transcription factor DksA from E. coli===
+
== 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]]
-
The line below this paragraph, {{ABSTRACT_PUBMED_15294156}}, adds the Publication Abstract to the page
+
Check<jmol>
-
(as it appears on PubMed at http://www.pubmed.gov), where 15294156 is the PubMed ID number.
+
<jmolCheckbox>
-
-->
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tj/1tjl_consurf.spt"</scriptWhenChecked>
-
{{ABSTRACT_PUBMED_15294156}}
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1TJL is a 10 chains structure of sequences from [http://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].
+
</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>
-
==Reference==
+
== References ==
-
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://www.ncbi.nlm.nih.gov/pubmed/15294156 15294156]
+
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Artsimovitch, I.]]
+
[[Category: Large Structures]]
-
[[Category: Perederina, A.]]
+
[[Category: Artsimovitch I]]
-
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+
[[Category: Perederina A]]
-
[[Category: Svetlov, V.]]
+
[[Category: Svetlov V]]
-
[[Category: Vassylyev, D G.]]
+
[[Category: Vassylyev DG]]
-
[[Category: Vassylyeva, M N.]]
+
[[Category: Vassylyeva MN]]
-
[[Category: Yokoyama, S.]]
+
[[Category: Yokoyama S]]
-
[[Category: Dksa]]
+
-
[[Category: Ppgpp]]
+
-
[[Category: Riken structural genomics/proteomics initiative]]
+
-
[[Category: Rna polymerase]]
+
-
[[Category: Rsgi]]
+
-
[[Category: Stringent response]]
+
-
[[Category: Structural genomic]]
+
-
[[Category: Transcription factor]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 14:06:38 2008''
+

Current revision

Crystal structure of transcription factor DksA from E. coli

PDB ID 1tjl

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1tjl"
Personal tools