+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDAB7 |
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Sample | Complex ComE-comcde
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Function / homology | Function and homology information |
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 ...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 ...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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDAB7 |
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-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-External links
Related items in Molecule of the Month |
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-Models
Model #253 | Type: atomic / Chi-square value: 1.473796 Search similar-shape structures of this assembly by Omokage search (details) |
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-Sample
Sample | Name: Complex ComE-comcde / Specimen concentration: 0.8 mg/ml / Entity id: 152 / 155 |
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Buffer | Name: 50 mM MES 500 mM NaCl 5% (v/v) Glycerol 5 mM β-mercaptoethanol 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 #155 | 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 ...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: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 1.82 mm | ||||||||||||||||||
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Detector | Name: AVIEX / Type: CCD | ||||||||||||||||||
Scan | Title: Complex ComE-comcde / Measurement date: Feb 11, 2011 / Storage temperature: 18 °C / Cell temperature: 18 °C / Exposure time: 1.2 sec. / Number of frames: 6 / Unit: 1/nm /
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Distance distribution function P(R) | Sofotware P(R): GNOM 4.6 / Number of points: 300 /
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Result | D max: 10.7 / Type of curve: sec Comments: Use of SAXS to describe the interaction between the phosphorylated mimetic mutant ComED58E of the response regulator ComE from S. pneumonia and its promoter region comcde. The complex is ...Comments: Use of SAXS to describe the interaction between the phosphorylated mimetic mutant ComED58E of the response regulator ComE from S. pneumonia and its promoter region comcde. The complex is constituted of one dimer of ComE and one monomer 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).
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