SASDAC7: Complex LytTR-comcde (comcde + Response regulator, LytTR)

Basic information

• Entry: Database: SASBDB / ID: SASDAC7

Sample

Complex LytTR-comcde

• comcde (DNA), Streptococcus pneumoniae
• Response regulator (protein), LytTR, Streptococcus pneumoniae

Function / homology

Function:

phosphorelay response regulator activity / DNA binding

Domain/homology:

: / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily

Component:

Response regulator

• Biological species: Streptococcus pneumoniae (bacteria)
• Citation: Journal: FEBS J / Year: 2015; Title: Modeling the ComD/ComE/comcde interaction network using small angle X-ray scattering.; Authors: Dyana Sanchez / Marion Boudes / Herman van Tilbeurgh / Dominique Durand / Sophie Quevillon-Cheruel / ; Abstract: The ComD-ComE two-component system controls the competence state of Streptococcus pneumoniae via the phospho-regulation of ComE, which fluctuates between monomeric and dimeric states. We previously showed that the non-phosphorylatable ComE(D) (58A) mutant is monomeric in solution, whereas the ComE(D) (58E) active mimic mutant dimerizes via its REC domains. The crystal structure of ComE(D) (58A) revealed an asymmetric dimer that may represent the activated form of ComE. Here, we investigated the binding between the catalytic domain of ComD, ComE and the promoter region comcde, using small angle X-ray scattering. ComD(catdom) is a dimer that adapts two monomers of ComE, one on each side, placing (Com) (E) D58 residue in front of (Com) (D) H248, a location that is convenient for the intermolecular transfer reaction of the phosphoryl group. The LytTR, ComE(D) (58A) and ComE(D) (58E) complexed with comcde are composed of two protein molecules per DNA duplex. Modeling the complexes against small angle X-ray scattering data indicated that ComE(D) (58E) bound to comcde forms a compact dimer similar to the crystal structure, whereas ComE(D) (58A) -comcde adopts more than one conformation with or without dimer contacts. The various oligomeric states of ComE induce different bending angles of the promoter, which provides a mechanistic scenario for the activation of ComE: the phosphorylation of ComE forces additional bending of comcde, and the release of this bending strain on DNA via the disruption of the ComE dimer may signal the shut-off of the competence state.; DATABASE: The molecular models and experimental SAXS data have been deposited on SASBDB (Small Angle Scattering Biological Data Bank) (see http://www.sasbdb.org/aboutSASBDB/) under the SAS codes SASDAA7, SASDAB7 and SASDAC7.

Contact author

• Dominique Durand

Models

• Model #254: ; Type: atomic / Software: SASREF / Chi-square value: 1.196836; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Complex LytTR-comcde; Purity method: size-exclusion high-performance liquid chromatography (SEC-HPLC) column.; Specimen concentration: 0.4 mg/ml; Concentration method: size-exclusion high-performance liquid chromatography (SEC-HPLC) column.; Entity id: 152 / 153
• Buffer: Name: MES / Concentration: 50.00 mM / pH: 6.2 ; Composition: 500 mM NaCl, 5% (vol/vol) glycerol, 5 mM β-mercaptoethanol

Entity #152

Type: DNA / Description: comcde / Formula weight: 23.5 / Source: Streptococcus pneumoniae
Sequence:

5AAGTACACT TTGGGAGAAA AAAATGACAG TTGAGAGAA3 3TTCATGTGA AACCCTCTTT TTTTACTGTC AACTCTCTT5

Entity #153

Name: LytTR / Type: protein / Description: Response regulator / Formula weight: 14.434 / Num. of mol.: 2 / Source: Streptococcus pneumoniae / References: UniProt: Q8DMW5
Sequence:

VVDYFDYNYK GNDLKIPYHD ILYIETTGVS HKLRIIGKNF AKEFYGTMTD IQEKDKHTQR FYSPHKSFLV NIGNIREIDR KNLEIVFYED HRCPISRLKI RKLKDILEKK SQKHHHHHH

Experimental information

• Beam: Instrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 1.82 mm
• Detector: Name: AVIEX / Type: CCD

Scan

Title: Complex LytTR-comcde / Measurement date: Jun 2, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 16 / Unit: 1/nm /

	Min	Max
Q	0.1014	4.0031

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 340 /

	Min	Max
Q	0.01042	0.3916
P(R) point	1	340
R	0	125

Result

D max: 12.5 / Type of curve: single_conc
Comments: Use of SAXS to describe the interaction between the LytTR domain of the response regulator ComE from S. pneumonia and the promoter region comcde. The complex is constituted of two monomers of LytTR and one molecule of comcde. The SAXS data were collected directly after elution through an on-line size-exclusion high-performance liquid chromatography (SEC-HPLC) column. The molecular weight is not estimated from I(0) because the concentration of the complex cannot be accurately determined. It is obtained from the macromolecule volume using the method developed by Craievich’s team (the SAXS Mow program).

	Experimental	Porod
MW	56 kDa	56 kDa
Volume	-	74 nm3

	P(R)	Guinier
Forward scattering, I0	0.02366	0.02362
Radius of gyration, Rg	3.62 nm	3.55 nm