Structural characterization of the circadian clock protein complex composed of KaiB and KaiC by inverse contrast-matching small-angle neutron scattering

Sugiyama, Masaaki; Yagi, Hirokazu; Ishii, Kentaro; Porcar, Lionel; Martel, Anne; Oyama, Katsuaki; Noda, Masanori; Yunoki, Yasuhiro; Murakami, Reiko; Inoue, Rintaro; Sato, Nobuhiro; Oba, Yojiro; Terauchi, Kazuki; Uchiyama, Susumu; Kato, Koichi

doi:10.1038/srep35567

Cited by 25 publications

(24 citation statements)

References 29 publications

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“…3, C and D). Consistent with a role in cooperative assembly of the KaiB-KaiC hexamer (50, 53), an R23A mutation in KaiB As (superscript “As” denotes proteins from Anabaena sp.) reduced its binding affinity for KaiC As (54).…”

Section: Kaib Forms a Hexameric Ring On The CI Domains Of Kaicmentioning

confidence: 86%

Structural basis of the day-night transition in a bacterial circadian clock

Tseng

Goularte

Chavan

et al. 2017

Science

161

249

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Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day. In cyanobacteria, timing is generated by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output signaling proteins, SasA and CikA, which transduce this rhythm to control gene expression. Here, we describe crystal and nuclear magnetic resonance structures of KaiB-KaiC, KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how the metamorphic properties of KaiB, a protein that adopts two distinct folds, and the post–adenosine triphosphate hydrolysis state of KaiC create a hub around which nighttime signaling events revolve, including inactivation of KaiA and reciprocal regulation of the mutually antagonistic signaling proteins, SasA and CikA.

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Section: Kaib Forms a Hexameric Ring On The CI Domains Of Kaicmentioning

confidence: 86%

Structural basis of the day-night transition in a bacterial circadian clock

Tseng

Goularte

Chavan

et al. 2017

Science

161

249

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“…It has been demonstrated that KaiB-KaiC complex formation is dependent on the phosphorylation state of KaiC. [40][41][42][43][44][45][46] For example, the recombinant KaiB protein associates with the WT or hyperphosphomimic KaiC protein in the absence of KaiA in vitro, whereas it associates much less with KaiC AA44,46 . Thus, complex formation between KaiB and KaiC would be important for generating the kaiA-less damped oscillation.…”

Section: Resonance Of Damped Oscillation In Response To External Cuesmentioning

confidence: 99%

Damped circadian oscillation in the absence of KaiA in Synechococcus

et al. 2020

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Proteins KaiA, KaiB and KaiC constitute a biochemical circadian oscillator in the cyanobacterium Synechococcus elongatus. It has been reported kaiA inactivation completely abolishes circadian oscillations. However, we show here that kaiBC promoter activity exhibits a damped, low-amplitude oscillation with a period of approximately 24 h in kaiA-inactivated strains. The damped rhythm resonates with external cycles with a period of 24-26 h, indicating that its natural frequency is similar to that of the circadian clock. Double-mutation experiments reveal that kaiC, kaiB, and sasA (encoding a KaiC-binding histidine kinase) are all required for the damped oscillation. Further analysis suggests that the kaiA-less damped transcriptional rhythm requires KaiB-KaiC complex formation and the transcriptiontranslation feedback loop, but not the KaiC phosphorylation cycle. Our results provide insights into mechanisms that could potentially underlie the diurnal/circadian behaviors observed in other bacterial species that possess kaiB and kaiC homologues but lack a kaiA homologue.

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“…This technique was pioneeringly applied to determine the spatial arrangements of 30 S ribosomal subunits [4] and recently sophisticated as exemplified by the application to quaternary structure analyses of a variety of protein complexes [5] , [6] , [7] , [8] . Deuteration-assisted SANS data in conjunction with crystallographic data has thus facilitated 3D modelling of quaternary structure views of protein complexes like the circadian clock protein complex, KaiB and KaiC [9] , and the large dodecameric aminopeptidase TET [10] .…”

Section: Introductionmentioning

confidence: 99%

Characterization of conformational deformation-coupled interaction between immunoglobulin G1 Fc glycoprotein and a low-affinity Fcγ receptor by deuteration-assisted small-angle neutron scattering

Yogo

Yanaka

Yagi

et al. 2017

Biochemistry and Biophysics Reports

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A recently developed integrative approach combining varied types of experimental data has been successfully applied to three-dimensional modelling of larger biomacromolecular complexes. Deuteration-assisted small-angle neutron scattering (SANS) plays a unique role in this approach by making it possible to observe selected components in the complex. It enables integrative modelling of biomolecular complexes based on building-block structures typically provided by X-ray crystallography. In this integrative approach, it is important to be aware of the flexible properties of the individual building blocks. Here we examine the ability of SANS to detect a subtle conformational change of a multidomain protein using the Fc portion of human immunoglobulin G (IgG) interacting with a soluble form of the low-affinity Fcγ receptor IIIb (sFcγRIIIb) as a model system. The IgG-Fc glycoprotein was subjected to SANS in the absence and presence of 75%-deuterated sFcγRIIIb, which was matched out in D2O solution. This inverse contrast-matching technique enabled selective observation of SANS from IgG-Fc, thereby detecting its subtle structural deformation induced by the receptor binding. The SANS data were successfully interpreted by considering previously reported crystallographic data and an equilibrium between free and sFcγRIIIb-bound forms. Our SANS data thus demonstrate the applicability of SANS in the integrative approach dealing with biomacromolecular complexes composed of weakly associated building blocks with conformational plasticity.

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Structural characterization of the circadian clock protein complex composed of KaiB and KaiC by inverse contrast-matching small-angle neutron scattering

Cited by 25 publications

References 29 publications

Structural basis of the day-night transition in a bacterial circadian clock

Structural basis of the day-night transition in a bacterial circadian clock

Damped circadian oscillation in the absence of KaiA in Synechococcus

Characterization of conformational deformation-coupled interaction between immunoglobulin G1 Fc glycoprotein and a low-affinity Fcγ receptor by deuteration-assisted small-angle neutron scattering

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