7khe

Escherichia coli RNA polymerase and rrnBP1 promoter pre-open complex with DksA/ppGppEscherichia coli RNA polymerase and rrnBP1 promoter pre-open complex with DksA/ppGpp

Structural highlights

7khe is a 9 chain structure with sequence from Escherichia coli K-12. This structure supersedes the now removed PDB entry 6wrg. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.58Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4] ^[5]

References

↑ Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, Foster JW, Gourse RL. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell. 2004 Aug 6;118(3):311-22. PMID:15294157 doi:http://dx.doi.org/10.1016/j.cell.2004.07.009
↑ Meddows TR, Savory AP, Grove JI, Moore T, Lloyd RG. RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double-strand breaks. Mol Microbiol. 2005 Jul;57(1):97-110. PMID:15948952 doi:http://dx.doi.org/10.1111/j.1365-2958.2005.04677.x
↑ Mallik P, Paul BJ, Rutherford ST, Gourse RL, Osuna R. DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J Bacteriol. 2006 Aug;188(16):5775-82. PMID:16885445 doi:http://dx.doi.org/10.1128/JB.00276-06
↑ Furman R, Sevostyanova A, Artsimovitch I. Transcription initiation factor DksA has diverse effects on RNA chain elongation. Nucleic Acids Res. 2012 Apr;40(8):3392-402. doi: 10.1093/nar/gkr1273. Epub 2011, Dec 30. PMID:22210857 doi:http://dx.doi.org/10.1093/nar/gkr1273
↑ Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell. 2004 Aug 6;118(3):297-309. PMID:15294156 doi:10.1016/j.cell.2004.06.030

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OCA

[1] Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, Foster JW, Gourse RL. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell. 2004 Aug 6;118(3):311-22. PMID:15294157 doi:http://dx.doi.org/10.1016/j.cell.2004.07.009

[2] Meddows TR, Savory AP, Grove JI, Moore T, Lloyd RG. RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double-strand breaks. Mol Microbiol. 2005 Jul;57(1):97-110. PMID:15948952 doi:http://dx.doi.org/10.1111/j.1365-2958.2005.04677.x

[3] Mallik P, Paul BJ, Rutherford ST, Gourse RL, Osuna R. DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J Bacteriol. 2006 Aug;188(16):5775-82. PMID:16885445 doi:http://dx.doi.org/10.1128/JB.00276-06

[4] Furman R, Sevostyanova A, Artsimovitch I. Transcription initiation factor DksA has diverse effects on RNA chain elongation. Nucleic Acids Res. 2012 Apr;40(8):3392-402. doi: 10.1093/nar/gkr1273. Epub 2011, Dec 30. PMID:22210857 doi:http://dx.doi.org/10.1093/nar/gkr1273

[5] Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell. 2004 Aug 6;118(3):297-309. PMID:15294156 doi:10.1016/j.cell.2004.06.030

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