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6kj6

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Revision as of 02:26, 11 April 2020

cryo-EM structure of Escherichia coli Crl transcription activation complex

6kj6, resolution 3.80Å

Structural highlights

6kj6 is a 10 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
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

[RPOC_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [CRL_ECOLC] Binds to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. Stimulates RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32. [RPOB_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [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] [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] [RPOS_ECOLI] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response. Controls, positively or negatively, the expression of several hundred genes, which are mainly involved in metabolism, transport, regulation and stress management.[HAMAP-Rule:MF_00959]^[1] ^[2] ^[3] ^[4] ^[5] Protects stationary phase cells from killing induced by endoribonuclease MazF.^[6]

Publication Abstract from PubMed

sigma(S) is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses including antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of sigma(S)-mediated transcription requires a sigma(S)-specific activator, Crl. In this study, we determined a 3.80 A cryo-EM structure of an Escherichia coli transcription activation complex (E. coli Crl-TAC) comprising E. coli sigma(S)-RNA polymerase (sigma(S)-RNAP) holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with domain 2 of sigma(S) (sigma(S)2) and the RNAP core enzyme, but does not contact promoter DNA. Results from subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) indicate that Crl stabilizes key structural motifs within sigma(S)2 to promote the assembly of the sigma(S)-RNAP holoenzyme and also to facilitate formation of an RNA polymerase-promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells.

Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor.,Xu J, Cui K, Shen L, Shi J, Li L, You L, Fang C, Zhao G, Feng Y, Yang B, Zhang Y Elife. 2019 Dec 17;8. pii: 50928. doi: 10.7554/eLife.50928. PMID:31846423^[7]

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

References

↑ Patten CL, Kirchhof MG, Schertzberg MR, Morton RA, Schellhorn HE. Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Mol Genet Genomics. 2004 Dec;272(5):580-91. Epub 2004 Nov 19. PMID:15558318 doi:http://dx.doi.org/10.1007/s00438-004-1089-2
↑ Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R. Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J Bacteriol. 2005 Mar;187(5):1591-603. PMID:15716429 doi:http://dx.doi.org/10.1128/JB.187.5.1591-1603.2005
↑ Rahman M, Hasan MR, Oba T, Shimizu K. Effect of rpoS gene knockout on the metabolism of Escherichia coli during exponential growth phase and early stationary phase based on gene expressions, enzyme activities and intracellular metabolite concentrations. Biotechnol Bioeng. 2006 Jun 20;94(3):585-95. PMID:16511888 doi:http://dx.doi.org/10.1002/bit.20858
↑ Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P. In vitro transcription profiling of the sigmaS subunit of bacterial RNA polymerase: re-definition of the sigmaS regulon and identification of sigmaS-specific promoter sequence elements. Nucleic Acids Res. 2011 Jul;39(13):5338-55. doi: 10.1093/nar/gkr129. Epub 2011, Mar 11. PMID:21398637 doi:http://dx.doi.org/10.1093/nar/gkr129
↑ Tanaka K, Takayanagi Y, Fujita N, Ishihama A, Takahashi H. Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coli. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3511-5. PMID:8475100
↑ Kolodkin-Gal I, Engelberg-Kulka H. The stationary-phase sigma factor sigma(S) is responsible for the resistance of Escherichia coli stationary-phase cells to mazEF-mediated cell death. J Bacteriol. 2009 May;191(9):3177-82. doi: 10.1128/JB.00011-09. Epub 2009 Feb 27. PMID:19251848 doi:http://dx.doi.org/10.1128/JB.00011-09
↑ Xu J, Cui K, Shen L, Shi J, Li L, You L, Fang C, Zhao G, Feng Y, Yang B, Zhang Y. Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor. Elife. 2019 Dec 17;8. pii: 50928. doi: 10.7554/eLife.50928. PMID:31846423 doi:http://dx.doi.org/10.7554/eLife.50928

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6kj6"

@@ Line 3: / Line 3: @@
 <SX load='6kj6' size='340' side='right' viewer='molstar' caption='[[6kj6]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6kj6]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KJ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KJ6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6kj6]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KJ6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KJ6 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='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=6kj6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kj6 OCA], [http://pdbe.org/6kj6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kj6 RCSB], [http://www.ebi.ac.uk/pdbsum/6kj6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kj6 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=6kj6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kj6 OCA], [http://pdbe.org/6kj6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kj6 RCSB], [http://www.ebi.ac.uk/pdbsum/6kj6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kj6 ProSAT]</span></td></tr>
 </table>
 == Function ==

6kj6

From Proteopedia

Revision as of 02:26, 11 April 2020

cryo-EM structure of Escherichia coli Crl transcription activation complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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