5w1t

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==X-ray crystal structure of Escherichia coli RNA polymerase and DksA complex==
==X-ray crystal structure of Escherichia coli RNA polymerase and DksA complex==
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<StructureSection load='5w1t' size='340' side='right' caption='[[5w1t]], [[Resolution|resolution]] 4.50&Aring;' scene=''>
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<StructureSection load='5w1t' size='340' side='right'caption='[[5w1t]], [[Resolution|resolution]] 4.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5w1t]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W1T FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5w1t]] is a 14 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=5W1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W1T FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4.5&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5vsw|5vsw]], [[5w1s|5w1s]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoD, alt, b3067, JW3039 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), dksA, b0145, JW0141 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5w1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w1t OCA], [https://pdbe.org/5w1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w1t RCSB], [https://www.ebi.ac.uk/pdbsum/5w1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w1t ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
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<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=5w1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w1t OCA], [http://pdbe.org/5w1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w1t RCSB], [http://www.ebi.ac.uk/pdbsum/5w1t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w1t ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://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> [[http://www.uniprot.org/uniprot/RPOZ_ECOLI RPOZ_ECOLI]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.[HAMAP-Rule:MF_00366] [[http://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] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[http://www.uniprot.org/uniprot/RPOD_ECOLI RPOD_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.
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[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]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DksA and ppGpp are the central players in the stringent response and mediate a complete reprogramming of the transcriptome. A major component of the response is a reduction in ribosome synthesis, which is accomplished by the synergistic action of DksA and ppGpp bound to RNA polymerase (RNAP) inhibiting transcription of rRNAs. Here, we report the X-ray crystal structures of Escherichia coli RNAP in complex with DksA alone and with ppGpp. The structures show that DksA accesses the template strand at the active site and the downstream DNA binding site of RNAP simultaneously and reveal that binding of the allosteric effector ppGpp reshapes the RNAP-DksA complex. The structural data support a model for transcriptional inhibition in which ppGpp potentiates the destabilization of open complexes by DksA. This work establishes a structural basis for understanding the pleiotropic effects of DksA and ppGpp on transcriptional regulation in proteobacteria.
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Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.,Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, Murakami KS Mol Cell. 2018 Mar 1;69(5):828-839.e5. doi: 10.1016/j.molcel.2018.01.035. Epub, 2018 Feb 22. PMID:29478808<ref>PMID:29478808</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5w1t" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Sigma factor 3D structures|Sigma factor 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Escherichia coli K-12]]
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[[Category: Ecoli]]
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[[Category: Large Structures]]
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[[Category: Molodtsov, V]]
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[[Category: Molodtsov V]]
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[[Category: Murakami, K S]]
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[[Category: Murakami KS]]
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[[Category: Dksa]]
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[[Category: Rna polymerase]]
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[[Category: Transferase]]
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Current revision

X-ray crystal structure of Escherichia coli RNA polymerase and DksA complex

PDB ID 5w1t

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