6IDO

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

• PDB DOI: https://doi.org/10.2210/pdb6IDO/pdb
• NAKB: 6IDO

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli, Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-09-10 Released: 2019-09-11 
• Deposition Author(s): Lou, Y.C., Chien, C.Y., Chen, C., Hsu, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.75 Å
• R-Value Free: 0.253 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Literature

Structural basis for -35 element recognition by sigma4chimera proteins and their interactions with PmrA response regulator.

Lou, Y.C., Chou, C.C., Yeh, H.H., Chien, C.Y., Sadotra, S., Hsu, C.H., Chen, C.

(2020) Proteins 88: 69-81

• PubMed: 31293000 
• DOI: https://doi.org/10.1002/prot.25768
• Primary Citation of Related Structures:  
  6IDO


• 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 ₄ ) to activate transcription. However, σ ₄ of σ ⁷⁰ appears to be poorly folded on its own. Here, by fusing σ ₄ with the RNA polymerase β-flap-tip-helix, we constructed two σ ₄ chimera proteins, one from σ ⁷⁰ $\left({\sigma }_{}^{}\right)$ 4 70 c and another from σ ^S $\left({\sigma }_{}^{}\right)$ 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 σ ₄ in the Escherichia coli RNA polymerase σ ^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 β-flap-tip-helix of ${\sigma }_{}^{}$ 4 70 c have a concurrent transient α-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 σ factors.

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Organizational Affiliation: 

Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.91 kDa 
• Atom Count: 2,570 
• Modelled Residue Count: 223 
• Deposited Residue Count: 292 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helix	A, D [auth B]	115	Escherichia coli, Klebsiella pneumoniae This entity is chimeric	Mutation(s): 1  Gene Names: rpoS
UniProt
Find proteins for A6TGP0 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TGP0  Go to UniProtKB:  A6TGP0
Find proteins for P13445 (Escherichia coli (strain K12)) Explore P13445  Go to UniProtKB:  P13445
UniProt Groups	A6TGP0P13445

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*TP*TP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*C)-3')	B [auth C], E	15	Klebsiella pneumoniae

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*AP*AP*TP*CP*G)-3')	C [auth D], F	16	Klebsiella pneumoniae

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.75 Å
• R-Value Free: 0.253 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.54	α = 90
b = 154.54	β = 90
c = 144.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
Coot	model building
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Lou, Y.C., Chien, C.Y., Chen, C., Hsu, C.H.

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description