regulation of cellular response to stress / phosphorelay signal transduction system / transcription regulator complex / sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding ...regulation of cellular response to stress / phosphorelay signal transduction system / transcription regulator complex / sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function
Journal: Science / Year: 2005 Title: Structural insights into the activity of enhancer-binding proteins. Authors: Mathieu Rappas / Jorg Schumacher / Fabienne Beuron / Hajime Niwa / Patricia Bordes / Sivaramesh Wigneshweraraj / Catherine A Keetch / Carol V Robinson / Martin Buck / Xiaodong Zhang / Abstract: Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic ...Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic electron microscopy (cryo-EM) a 20 angstrom resolution structure of an activator, phage shock protein F [PspF(1-275)], which is bound to an ATP transition state analog in complex with its basal factor, sigma54. By fitting the crystal structure of PspF(1-275) at 1.75 angstroms into the EM map, we identified two loops involved in binding sigma54. Comparing enhancer-binding structures in different nucleotide states and mutational analysis led us to propose nucleotide-dependent conformational changes that free the loops for association with sigma54.
Resolution: 1.75→100 Å / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED AS ALANINES.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20785
1410
5 %
RANDOM
Rwork
0.18041
-
-
-
obs
0.18041
26860
95.5 %
-
Solvent computation
Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 23.028 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.57 Å2
-0.28 Å2
0 Å2
2-
-
-0.57 Å2
0 Å2
3-
-
-
0.85 Å2
Refinement step
Cycle: LAST / Resolution: 1.75→100 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1917
0
0
196
2113
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
c_bond_d
0.022
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.696
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
5.37
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
1.38
1.5
X-RAY DIFFRACTION
c_mcangle_it
2.443
2
X-RAY DIFFRACTION
c_scbond_it
3.54
3
X-RAY DIFFRACTION
c_scangle_it
5.855
4.5
LS refinement shell
Resolution: 1.75→1.796 Å / Total num. of bins used: 20
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