2qke

From Proteopedia

(Difference between revisions)

Current revision

Wild Type Crystal Structure of Full Length Circadian Clock Protein KaiB from Thermosynechococcus elongatus BP-1

Structural highlights

2qke is a 6 chain structure with sequence from Synechococcus elongatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KAIB_THEVB Key component of the KaiABC oscillator complex, which constitutes the main circadian regulator in cyanobacteria (PubMed:24112939, PubMed:16227211, PubMed:28302851). Its composition changes during the circadian cycle to control KaiC phosphorylation. KaiA stimulates KaiC autophosphorylation, while KaiB sequesters KaiA, leading to KaiC autodephosphorylation. KaiA binding to KaiC yields KaiA(2-4):KaiC(6) complexes which stimulate KaiC autophosphorylation. Phospho-Ser-431 KaiC accumulation triggers binding of KaiB to form the KaiB(6):KaiC(6) complex, leading to changes in the output regulators CikA and SasA (PubMed:28302851). KaiB switches to a thioredoxin-like fold (KaiB(fs)) in complex with KaiC (PubMed:26113641, PubMed:28302851). KaiB(6):KaiC(6) formation exposes a site for KaiA binding that sequesters KaiA from the CII domain, making the KaiC(6):KaiB(6):KaiA(12) complex that results in KaiC autodephosphorylation. Complete dephosphorylation of KaiC leads to dissociation of KaiA(2):KaiB(1), completing 1 cycle of the Kai oscillator (PubMed:28302851).^[1] ^[2] ^[3] ^[4] A metamorphic protein which reversibly switches between an inactive tetrameric fold and a rare, thioredoxin-like monomeric fold (KaiB(fs)). KaiB(fs) binds phospho-KaiC, KaiA and CikA. KaiA and CikA compete for binding to KaiB(fs), and KaiB(fs) and SasA compete for binding to KaiC, thus the clock oscillator and output signal pathway are tightly coupled.[HAMAP-Rule:MF_01835]^[5] ^[6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The circadian clock of the cyanobacterium Synechococcus elongatus can be reconstituted in vitro by the KaiA, KaiB and KaiC proteins in the presence of ATP. The principal clock component, KaiC, undergoes regular cycles between hyper- and hypo-phosphorylated states with a period of ca. 24 h that is temperature compensated. KaiA enhances KaiC phosphorylation and this enhancement is antagonized by KaiB. Throughout the cycle Kai proteins interact in a dynamic manner to form complexes of different composition. We present a three-dimensional model of the S. elongatus KaiB-KaiC complex based on X-ray crystallography, negative-stain and cryo-electron microscopy, native gel electrophoresis and modelling techniques. We provide experimental evidence that KaiB dimers interact with KaiC from the same side as KaiA and for a conformational rearrangement of the C-terminal regions of KaiC subunits. The enlarged central channel and thus KaiC subunit separation in the C-terminal ring of the hexamer is consistent with KaiC subunit exchange during the dephosphorylation phase. The proposed binding mode of KaiB explains the observation of simultaneous binding of KaiA and KaiB to KaiC, and provides insight into the mechanism of KaiB's antagonism of KaiA.

Structural model of the circadian clock KaiB-KaiC complex and mechanism for modulation of KaiC phosphorylation.,Pattanayek R, Williams DR, Pattanayek S, Mori T, Johnson CH, Stewart PL, Egli M EMBO J. 2008 Jun 18;27(12):1767-78. Epub 2008 May 22. PMID:18497745^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Iwase R, Imada K, Hayashi F, Uzumaki T, Morishita M, Onai K, Furukawa Y, Namba K, Ishiura M. Functionally important substructures of circadian clock protein KaiB in a unique tetramer complex. J Biol Chem. 2005 Dec 30;280(52):43141-9. Epub 2005 Oct 13. PMID:16227211 doi:http://dx.doi.org/10.1074/jbc.M503360200
↑ Tseng R, Chang YG, Bravo I, Latham R, Chaudhary A, Kuo NW, Liwang A. Cooperative KaiA-KaiB-KaiC interactions affect KaiB/SasA competition in the circadian clock of cyanobacteria. J Mol Biol. 2014 Jan 23;426(2):389-402. PMID:24112939 doi:10.1016/j.jmb.2013.09.040
↑ Chang YG, Cohen SE, Phong C, Myers WK, Kim YI, Tseng R, Lin J, Zhang L, Boyd JS, Lee Y, Kang S, Lee D, Li S, Britt RD, Rust MJ, Golden SS, LiWang A. Circadian rhythms. A protein fold switch joins the circadian oscillator to clock output in cyanobacteria. Science. 2015 Jul 17;349(6245):324-8. PMID:26113641 doi:10.1126/science.1260031
↑ Tseng R, Goularte NF, Chavan A, Luu J, Cohen SE, Chang YG, Heisler J, Li S, Michael AK, Tripathi S, Golden SS, LiWang A, Partch CL. Structural basis of the day-night transition in a bacterial circadian clock. Science. 2017 Mar 17;355(6330):1174-1180. doi: 10.1126/science.aag2516. Epub 2017, Mar 16. PMID:28302851 doi:http://dx.doi.org/10.1126/science.aag2516
↑ Chang YG, Cohen SE, Phong C, Myers WK, Kim YI, Tseng R, Lin J, Zhang L, Boyd JS, Lee Y, Kang S, Lee D, Li S, Britt RD, Rust MJ, Golden SS, LiWang A. Circadian rhythms. A protein fold switch joins the circadian oscillator to clock output in cyanobacteria. Science. 2015 Jul 17;349(6245):324-8. PMID:26113641 doi:10.1126/science.1260031
↑ Tseng R, Goularte NF, Chavan A, Luu J, Cohen SE, Chang YG, Heisler J, Li S, Michael AK, Tripathi S, Golden SS, LiWang A, Partch CL. Structural basis of the day-night transition in a bacterial circadian clock. Science. 2017 Mar 17;355(6330):1174-1180. doi: 10.1126/science.aag2516. Epub 2017, Mar 16. PMID:28302851 doi:http://dx.doi.org/10.1126/science.aag2516
↑ Pattanayek R, Williams DR, Pattanayek S, Mori T, Johnson CH, Stewart PL, Egli M. Structural model of the circadian clock KaiB-KaiC complex and mechanism for modulation of KaiC phosphorylation. EMBO J. 2008 Jun 18;27(12):1767-78. Epub 2008 May 22. PMID:18497745 doi:10.1038/emboj.2008.104

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2qke"

Categories: Large Structures | Synechococcus elongatus | Egli M | Pattanayek R | Pattanayek S

@@ Line 1: / Line 1: @@
 ==Wild Type Crystal Structure of Full Length Circadian Clock Protein KaiB from Thermosynechococcus elongatus BP-1==
-<StructureSection load='2qke' size='340' side='right' caption='[[2qke]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='2qke' size='340' side='right'caption='[[2qke]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qke]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechococcus_elongatus Synechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QKE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qke]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_elongatus Synechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QKE FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vgl|1vgl]], [[1r5p|1r5p]], [[1wwj|1wwj]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qke OCA], [http://pdbe.org/2qke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qke RCSB], [http://www.ebi.ac.uk/pdbsum/2qke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qke ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qke OCA], [https://pdbe.org/2qke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qke RCSB], [https://www.ebi.ac.uk/pdbsum/2qke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qke ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KAIB_THEEB KAIB_THEEB]] Component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. The KaiABC complex may act as a promoter-non-specific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. In the complex, it decreases the phosphorylation status of KaiC. It has no effect on KaiC by itself, but instead needs the presence of both KaiA and KaiC, suggesting that it acts by antagonizing the interaction between KaiA and KaiC.[HAMAP-Rule:MF_01835]
+[https://www.uniprot.org/uniprot/KAIB_THEVB KAIB_THEVB] Key component of the KaiABC oscillator complex, which constitutes the main circadian regulator in cyanobacteria (PubMed:24112939, PubMed:16227211, PubMed:28302851). Its composition changes during the circadian cycle to control KaiC phosphorylation. KaiA stimulates KaiC autophosphorylation, while KaiB sequesters KaiA, leading to KaiC autodephosphorylation. KaiA binding to KaiC yields KaiA(2-4):KaiC(6) complexes which stimulate KaiC autophosphorylation. Phospho-Ser-431 KaiC accumulation triggers binding of KaiB to form the KaiB(6):KaiC(6) complex, leading to changes in the output regulators CikA and SasA (PubMed:28302851). KaiB switches to a thioredoxin-like fold (KaiB(fs)) in complex with KaiC (PubMed:26113641, PubMed:28302851). KaiB(6):KaiC(6) formation exposes a site for KaiA binding that sequesters KaiA from the CII domain, making the KaiC(6):KaiB(6):KaiA(12) complex that results in KaiC autodephosphorylation. Complete dephosphorylation of KaiC leads to dissociation of KaiA(2):KaiB(1), completing 1 cycle of the Kai oscillator (PubMed:28302851).<ref>PMID:16227211</ref> <ref>PMID:24112939</ref> <ref>PMID:26113641</ref> <ref>PMID:28302851</ref>   A metamorphic protein which reversibly switches between an inactive tetrameric fold and a rare, thioredoxin-like monomeric fold (KaiB(fs)). KaiB(fs) binds phospho-KaiC, KaiA and CikA. KaiA and CikA compete for binding to KaiB(fs), and KaiB(fs) and SasA compete for binding to KaiC, thus the clock oscillator and output signal pathway are tightly coupled.[HAMAP-Rule:MF_01835]<ref>PMID:26113641</ref> <ref>PMID:28302851</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 30: / Line 30: @@
 ==See Also==
-*[[Circadian clock protein|Circadian clock protein]]
+*[[Circadian clock protein 3D structures|Circadian clock protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Synechococcus elongatus]]
-[[Category: Egli, M]]
+[[Category: Egli M]]
-[[Category: Pattanayek, R]]
+[[Category: Pattanayek R]]
-[[Category: Pattanayek, S]]
+[[Category: Pattanayek S]]
-[[Category: Circadian clock protein]]
-[[Category: Cyanobacterial circadian clock protein]]

2qke

From Proteopedia

Current revision

Wild Type Crystal Structure of Full Length Circadian Clock Protein KaiB from Thermosynechococcus elongatus BP-1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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