Proteopedia

6ido

Crystal structure of Klebsiella pneumoniae sigma4 of sigmaS fusing with the RNA polymerase beta-flap-tip-helix in complex with -35 element DNACrystal structure of Klebsiella pneumoniae sigma4 of sigmaS fusing with the RNA polymerase beta-flap-tip-helix in complex with -35 element DNA

Structural highlights

6ido is a 6 chain structure with sequence from Escherichia coli and Klebsiella pneumoniae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.748Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPOB_KLEP7 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321]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

In class II transcription activation, the transcription factor normally binds to the promoter near the -35 position and contacts the domain 4 of sigma factors (sigma4 ) to activate transcription. However, sigma4 of sigma(70) appears to be poorly folded on its own. Here, by fusing sigma4 with the RNA polymerase beta-flap-tip-helix, we constructed two sigma4 chimera proteins, one from sigma(70) sigma 4 70 c and another from sigma(S) sigma 4 S c of Klebsiella pneumoniae. The two chimera proteins well folded into a monomeric form with strong binding affinities for -35 element DNA. Determining the crystal structure of sigma 4 S c in complex with -35 element DNA revealed that sigma 4 S c adopts a similar structure as sigma4 in the Escherichia coli RNA polymerase sigma(S) holoenzyme and recognizes -35 element DNA specifically by several conserved residues from the helix-turn-helix motif. By using nuclear magnetic resonance (NMR), sigma 4 70 c was demonstrated to recognize -35 element DNA similar to sigma 4 S c . Carr-Purcell-Meiboom-Gill relaxation dispersion analyses showed that the N-terminal helix and the beta-flap-tip-helix of sigma 4 70 c have a concurrent transient alpha-helical structure and DNA binding reduced the slow dynamics on sigma 4 70 c . Finally, only sigma 4 70 c was shown to interact with the response regulator PmrA and its promoter DNA. The chimera proteins are capable of -35 element DNA recognition and can be used for study with transcription factors or other factors that interact with domain 4 of sigma factors.

Structural basis for -35 element recognition by sigma4 chimera proteins and their interactions with PmrA response regulator.,Lou YC, Chou CC, Yeh HH, Chien CY, Sadotra S, Hsu CH, Chen C Proteins. 2020 Jan;88(1):69-81. doi: 10.1002/prot.25768. Epub 2019 Jul 22. PMID:31293000[7]

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

References

  1. ↑ 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
  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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ Lou YC, Chou CC, Yeh HH, Chien CY, Sadotra S, Hsu CH, Chen C. Structural basis for -35 element recognition by sigma4 chimera proteins and their interactions with PmrA response regulator. Proteins. 2020 Jan;88(1):69-81. doi: 10.1002/prot.25768. Epub 2019 Jul 22. PMID:31293000 doi:http://dx.doi.org/10.1002/prot.25768

6ido, resolution 3.75Å

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