6IDO

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

Summary for 6IDO

• Entry DOI: 10.2210/pdb6ido/pdb
• Descriptor: RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helix, DNA (5'-D(P*GP*AP*TP*TP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*C)-3'), DNA (5'-D(P*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*AP*AP*TP*CP*G)-3') (3 entities in total)
• Functional Keywords: sigma4, sigmas, -35 element dna, transcription
• Biological source: Escherichia coli; More
• Total number of polymer chains: 6
• Total formula weight: 44907.74

Authors

Lou, Y.C.,Chien, C.Y.,Chen, C.,Hsu, C.H. (deposition date: 2018-09-10, release date: 2019-09-11, Last modification date: 2023-11-22)

Primary citation

Lou, Y.C.,Chou, C.C.,Yeh, H.H.,Chien, C.Y.,Sadotra, S.,Hsu, C.H.,Chen, C.
Structural basis for -35 element recognition by sigma4chimera proteins and their interactions with PmrA response regulator.
Proteins, 88:69-81, 2020

PubMed Abstract: In class II transcription activation, the transcription factor normally binds to the promoter near the -35 position and contacts the domain 4 of σ factors (σ ) to activate transcription. However, σ of σ appears to be poorly folded on its own. Here, by fusing σ with the RNA polymerase β-flap-tip-helix, we constructed two σ chimera proteins, one from σ and another from σ 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 in complex with -35 element DNA revealed that adopts a similar structure as σ in the Escherichia coli RNA polymerase σ holoenzyme and recognizes -35 element DNA specifically by several conserved residues from the helix-turn-helix motif. By using nuclear magnetic resonance (NMR), was demonstrated to recognize -35 element DNA similar to . Carr-Purcell-Meiboom-Gill relaxation dispersion analyses showed that the N-terminal helix and the β-flap-tip-helix of have a concurrent transient α-helical structure and DNA binding reduced the slow dynamics on . Finally, only 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 σ factors.

PubMed: 31293000
DOI: 10.1002/prot.25768

Experimental method

X-RAY DIFFRACTION (3.748 Å)