1vgl

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of tetrameric KaiB from T.elongatus BP-1

Structural highlights

1vgl is a 4 chain structure with sequence from Thermosynechococcus vestitus BP-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:
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

KaiB is a component of the circadian clock molecular machinery in cyanobacteria, which are the simplest organisms that exhibit circadian rhythms. Here we report the x-ray crystal structure of KaiB from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. The KaiB crystal diffracts at a resolution of 2.6 A and includes four subunits organized as a dimer of dimers, each composed of two non-equivalent subunits. The overall shape of the tetramer is an elongated hexagonal plate, with a single positively charged cleft flanked by two negatively charged ridges whose surfaces includes several terminal chains. Site-directed mutagenesis of Synechococcus KaiB confirmed that alanine substitution of residues Lys-11 or Lys-43 in the cleft, or deletion of C-terminal residues 95-108, which forms part of the ridges, strongly weakens in vivo circadian rhythms. Characteristics of KaiB deduced from the x-ray crystal structure were also confirmed by physicochemical measurements of KaiB in solution. These data suggest that the positively charged cleft and flanking negatively charged ridges in KaiB are essential for the biological function of KaiB in the circadian molecular machinery in cyanobacteria.

Functionally important substructures of circadian clock protein KaiB in a unique tetramer complex.,Iwase R, Imada K, Hayashi F, Uzumaki T, Morishita M, Onai K, Furukawa Y, Namba K, Ishiura M J Biol Chem. 2005 Dec 30;280(52):43141-9. Epub 2005 Oct 13. PMID:16227211^[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
↑ 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

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/1vgl"

@@ Line 3: / Line 3: @@
 <StructureSection load='1vgl' size='340' side='right'caption='[[1vgl]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1vgl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Theeb Theeb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VGL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1vgl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VGL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></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]] 2.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></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=1vgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vgl OCA], [https://pdbe.org/1vgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vgl RCSB], [https://www.ebi.ac.uk/pdbsum/1vgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vgl ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://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 36: / Line 37: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Theeb]]
+[[Category: Thermosynechococcus vestitus BP-1]]
-[[Category: Hayashi, F]]
+[[Category: Hayashi F]]
-[[Category: Imada, K]]
+[[Category: Imada K]]
-[[Category: Ishiura, M]]
+[[Category: Ishiura M]]
-[[Category: Iwase, R]]
+[[Category: Iwase R]]
-[[Category: Namba, K]]
+[[Category: Namba K]]
-[[Category: Uzumaki, T]]
+[[Category: Uzumaki T]]
-[[Category: Circadian clock protein]]

1vgl

From Proteopedia

Current revision

Crystal structure of tetrameric KaiB from T.elongatus BP-1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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