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6c9y

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Revision as of 23:38, 10 April 2020

Cryo-EM structure of E. coli RNAP sigma70 holoenzyme

6c9y, resolution 4.25Å

Structural highlights

6c9y is a 6 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	rpoA, pez, phs, sez, b3295, JW3257 (ECOLI), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 (ECOLI), rpoC, tabB, b3988, JW3951 (ECOLI), rpoZ, b3649, JW3624 (ECOLI), rpoD, alt, b3067, JW3039 (ECOLI)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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] [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] [RPOC_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [RPOB_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [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.

Publication Abstract from PubMed

First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In Escherichia coli, a primary sigma70 factor form the RNAP holoenzyme to express housekeeping genes. The sigma70 contains a large insertion at between the conserved regions 1.2 and 2.1, the sigma non-conserved region (sigmaNCR), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP sigma70 holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 A resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between R157 residue in the sNCR and promoter DNA just upstream of the -10 element, which was not observed in a previously determined E. coli RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography due to restraint of crystal packing effect. Disruption of the sNCR and DNA interaction by the amino acid substitutions (R157A/E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the sNCR and DNA interaction is conserved in proteobacteria and RNAP in other bacteria replace its role with a transcription factor.

Cryo-EM structure of Escherichia coli sigma(70) RNAP and promoter DNA complex revealed a role of sigma non-conserved region during the open complex formation.,Narayanan A, Vago FS, Li K, Qayyum MZ, Yernool D, Jiang W, Murakami KS J Biol Chem. 2018 Mar 26. pii: RA118.002161. doi: 10.1074/jbc.RA118.002161. PMID:29581236^[1]

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

References

↑ Narayanan A, Vago FS, Li K, Qayyum MZ, Yernool D, Jiang W, Murakami KS. Cryo-EM structure of Escherichia coli sigma(70) RNAP and promoter DNA complex revealed a role of sigma non-conserved region during the open complex formation. J Biol Chem. 2018 Mar 26. pii: RA118.002161. doi: 10.1074/jbc.RA118.002161. PMID:29581236 doi:http://dx.doi.org/10.1074/jbc.RA118.002161

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6c9y"

@@ Line 3: / Line 3: @@
 <SX load='6c9y' size='340' side='right' viewer='molstar' caption='[[6c9y]], [[Resolution|resolution]] 4.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6c9y]] is a 6 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=6C9Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C9Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6c9y]] is a 6 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=6C9Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6C9Y FirstGlance]. <br>
-</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>
+</td></tr><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>
 <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]), rpoZ, b3649, JW3624 ([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])</td></tr>
 <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>
-<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=6c9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c9y OCA], [http://pdbe.org/6c9y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c9y RCSB], [http://www.ebi.ac.uk/pdbsum/6c9y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c9y ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6c9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c9y OCA], [http://pdbe.org/6c9y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c9y RCSB], [http://www.ebi.ac.uk/pdbsum/6c9y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c9y ProSAT]</span></td></tr>
 </table>
 == Function ==

6c9y

From Proteopedia

Revision as of 23:38, 10 April 2020

Cryo-EM structure of E. coli RNAP sigma70 holoenzyme

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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