1xs9: Difference between revisions

Latest revision as of 07:57, 15 May 2024

A MODEL OF THE TERNARY COMPLEX FORMED BETWEEN MARA, THE ALPHA-CTD OF RNA POLYMERASE AND DNA

Structural highlights

1xs9 is a 4 chain structure with sequence from Escherichia coli. This structure supersedes the now removed PDB entry 1ti9. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MARA_ECOLI May be a transcriptional activator of genes involved in the multiple antibiotic resistance (Mar) phenotype. It can also activate genes such as sodA, zwf and micF.

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

The transcriptional activator, MarA, interacts with RNA polymerase (RNAP) to activate promoters of the mar regulon. Here, we identify the interacting surfaces of MarA and of the carboxy-terminal domain of the alpha subunit of RNAP (alpha-CTD) by NMR-based chemical shift mapping. Spectral changes were monitored for a MarA-DNA complex upon titration with alpha-CTD, and for alpha-CTD upon titration with MarA-DNA. The mapping results were confirmed by mutational studies and retention chromatography. A model of the ternary complex shows that alpha-CTD uses a '265-like determinant' to contact MarA at a surface distant from the DNA. This is unlike the interaction of alpha-CTD with the CRP or Fis activators where the '265 determinant' contacts DNA while another surface of the same alpha-CTD molecule contacts the activator. These results reveal a new versatility for alpha-CTD in transcriptional activation.

Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA.,Dangi B, Gronenborn AM, Rosner JL, Martin RG Mol Microbiol. 2004 Oct;54(1):45-59. PMID:15458404^[1]

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

References

↑ Dangi B, Gronenborn AM, Rosner JL, Martin RG. Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA. Mol Microbiol. 2004 Oct;54(1):45-59. PMID:15458404 doi:10.1111/j.1365-2958.2004.04250.x

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OCA

[1] Dangi B, Gronenborn AM, Rosner JL, Martin RG. Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA. Mol Microbiol. 2004 Oct;54(1):45-59. PMID:15458404 doi:10.1111/j.1365-2958.2004.04250.x

[1]

@@ Line 1: / Line 1: @@
 ==A MODEL OF THE TERNARY COMPLEX FORMED BETWEEN MARA, THE ALPHA-CTD OF RNA POLYMERASE AND DNA==
-<StructureSection load='1xs9' size='340' side='right'caption='[[1xs9]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='1xs9' size='340' side='right'caption='[[1xs9]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xs9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ti9 1ti9]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XS9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xs9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ti9 1ti9]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XS9 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">marA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoA, pez, phs, sez ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=1xs9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xs9 OCA], [https://pdbe.org/1xs9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xs9 RCSB], [https://www.ebi.ac.uk/pdbsum/1xs9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xs9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] [[https://www.uniprot.org/uniprot/MARA_ECOLI MARA_ECOLI]] May be a transcriptional activator of genes involved in the multiple antibiotic resistance (Mar) phenotype. It can also activate genes such as sodA, zwf and micF.
+[https://www.uniprot.org/uniprot/MARA_ECOLI MARA_ECOLI] May be a transcriptional activator of genes involved in the multiple antibiotic resistance (Mar) phenotype. It can also activate genes such as sodA, zwf and micF.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: DNA-directed RNA polymerase]]
 [[Category: Large Structures]]
-[[Category: Dangi, B]]
+[[Category: Dangi B]]
-[[Category: Gronenborn, A M]]
+[[Category: Gronenborn AM]]
-[[Category: Martin, R G]]
+[[Category: Martin RG]]
-[[Category: Rosner, J L]]
+[[Category: Rosner JL]]
-[[Category: Mara]]
-[[Category: Protein-dna complex]]
-[[Category: Rna polymerase]]
-[[Category: Ternary complex]]
-[[Category: Transcription-dna complex]]

1xs9: Difference between revisions

Latest revision as of 07:57, 15 May 2024

A MODEL OF THE TERNARY COMPLEX FORMED BETWEEN MARA, THE ALPHA-CTD OF RNA POLYMERASE AND DNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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