SASDAA7: Heterotetramer of histidine protein kinase and response regulator

Basic information

• Entry: Database: SASBDB / ID: SASDAA7

Sample

Heterotetramer of histidine protein kinase and response regulator

• Histidine protein kinase (protein), ComD, Streptococcus pneumoniae
• Response regulator (protein), ComE, Streptococcus pneumoniae

Function / homology

Function:

Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor / phosphorelay response regulator activity / kinase activity / membrane => GO:0016020 / DNA binding / identical protein binding

Domain/homology:

Sensor histidine kinase NatK, C-terminal domain / GHKL domain / : / 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 / Histidine kinase/HSP90-like ATPase superfamily

Component:

Histidine protein kinase / 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 #252: ; Type: atomic / Software: BUNCH+PD2 / Radius of dummy atoms: 1.90 A / Chi-square value: 0.978121; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Heterotetramer of histidine protein kinase and response regulator; Specimen concentration: 0.40-1.10 / Entity id: 150 / 151
• Buffer: Name: Tris / Concentration: 20.00 mM / pH: 7.5 ; Composition: 200 mM NaCl, 5% (vol/vol) glycerol and 5 mM β-mercaptoethanol

Entity #150

Name: ComD / Type: protein / Description: Histidine protein kinase / Formula weight: 26.912 / Num. of mol.: 2 / Source: Streptococcus pneumoniae / References: UniProt: Q8DMW4
Sequence:

MEIALKQKKF EQKHLQNYID EIVGLYNEIR GFRHDYAGML VSMQMAIDSG NLQEIDRIYN EVLVKANHKL RSDKYTYFDL NNIEDSALRS LVAQSIVYAR NNGVEFTLEV KDTITKLPIE LLDLVRIMSV LLNNAVEGSA DSYKKQMEVA VIKMETETVI VIQNSCKMTM TPSGDLFALG FSTKGRNRGV GLNNVKELLD KYNNIILETE MEGSTFRQII RFKREFEHHH HHH

Entity #151

Name: ComE / Type: protein / Description: Response regulator / Formula weight: 30.736 / Num. of mol.: 2 / Source: Streptococcus pneumoniae / References: UniProt: Q8DMW5
Sequence:

MKVLILEDVI EHQVRLERIL DEISKESNIP ISYKTTGKVR EFEEYIENDE VNQLYFLAID IHGIEKKGFE VAQLIRHYNP YAIIVFITSR SEFATLTYKY QVSALDFVDK DINDEMFKKR IEQNIFYTKS MLLENEDVVD YFDYNYKGND LKIPYHDILY IETTGVSHKL RIIGKNFAKE FYGTMTDIQE KDKHTQRFYS PHKSFLVNIG NIREIDRKNL EIVFYEDHRC PISRLKIRKL KDILEKKSQK HHHHHH

Experimental information

• Beam: Instrument name: Bruker Nanostar / City: Orsay / 国: France / Type of source: X-ray in house / Wavelength: 0.154 Å / Dist. spec. to detc.: 0.7 mm
• Detector: Name: VANTEC

Scan

Title: Complex ComD-ComE / Measurement date: May 16, 2012 / Storage temperature: 4 °C / Cell temperature: 4 °C / Exposure time: 1200 sec. / Number of frames: 32 / Unit: 1/nm /

	Min	Max
Q	0.1138	4.0098

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 270 /

	Min	Max
Q	0.01423	0.3967
P(R) point	5	274
R	0	160

Result

D max: 16 / Type of curve: merged / Standard: water
Comments: Use of SAXS to describe the interaction between ComD and ComE, the two-component system which regulates the competence in S. pneumoniae. The molecular weight is not estimated from I(0) due to the absence of tryptophan in ComE. It is obtained from the macromolecule volume by using the method developed by Craievich's team (the SAXS Mow program).

	Experimental	Porod
MW	116 kDa	116 kDa
Volume	-	175 nm3

	P(R)	Guinier
Forward scattering, I0	0.07508	0.07466
Radius of gyration, Rg	4.12 nm	3.98 nm