scholarly journals Crystal Structure of Circadian Clock Protein KaiA fromSynechococcus elongatus

2004 ◽  
Vol 279 (19) ◽  
pp. 20511-20518 ◽  
Author(s):  
Sheng Ye ◽  
Ioannis Vakonakis ◽  
Thomas R. Ioerger ◽  
Andy C. LiWang ◽  
James C. Sacchettini
Keyword(s):  
Crystal Structure ◽  
Circadian Clock ◽  
Binding Site ◽  
Regulation Mechanism ◽  
Response Regulators ◽  
Dimer Interface ◽  
Helix Bundle ◽  
Bacterial Response ◽  
Four Helix Bundle ◽  
Clock Protein

The circadian clock found inSynechococcus elongatus, the most ancient circadian clock, is regulated by the interaction of three proteins, KaiA, KaiB, and KaiC. While the precise function of these proteins remains unclear, KaiA has been shown to be a positive regulator of the expression of KaiB and KaiC. The 2.0-Å structure of KaiA ofS. elongatusreported here shows that the protein is composed of two independently folded domains connected by a linker. The NH2-terminalpseudo-receiver domain has a similar fold with that of bacterial response regulators, whereas the COOH-terminal four-helix bundle domain is novel and forms the interface of the 2-fold-related homodimer. The COOH-terminal four-helix bundle domain has been shown to contain the KaiC binding site. The structure suggests that the KaiB binding site is covered in the dimer interface of the KaiA “closed” conformation, observed in the crystal structure, which suggests an allosteric regulation mechanism.

scholarly journals Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9

2020 ◽  
Author(s):  
D. R. Littler ◽  
B. S. Gully ◽  
R. N. Colson ◽  
J Rossjohn
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Peptide Binding ◽  
Structural Protein ◽  
Dimer Interface ◽  
X Ray ◽  
3C Protease ◽  
Peptide Binding Site ◽  
High Level ◽  
Viral Genomic Rna

AbstractMany of the proteins produced by SARS-CoV-2 have related counterparts across the Severe Acute Respiratory Syndrome (SARS-CoV) family. One such protein is non-structural protein 9 (Nsp9), which is thought to mediate both viral replication and virulence. Current understanding suggests that Nsp9 is involved in viral genomic RNA reproduction. Nsp9 is thought to bind RNA via a fold that is unique to this class of betacoronoaviruses although the molecular basis for this remains ill-defined. We sought to better characterise the SARS-CoV-2 Nsp9 protein and subsequently solved its X-ray crystal structure, in an apo-form and, unexpectedly, in a peptide-bound form with a sequence originating from a rhinoviral 3C protease sequence (LEVL). The structure of the SARS-CoV-2 Nsp9 revealed the high level of structural conservation within the Nsp9 family. The exogenous peptide binding site is close to the dimer interface and impacted on the relative juxtaposition of the monomers within the homodimer. Together we have established a protocol for the production of SARS-CoV-2 Nsp9, determined its structure and identified a peptide-binding site that may warrant further study from the perspective of understanding Nsp9 function.

scholarly journals Crystal structure of the C-terminal four-helix bundle of the potassium channel KCa3.1

PLoS ONE ◽  
2018 ◽  
Vol 13 (6) ◽  
pp. e0199942 ◽  
Author(s):  
Tianyang Ji ◽  
Senena Corbalán-García ◽  
Stevan R. Hubbard
Keyword(s):  
Crystal Structure ◽  
Potassium Channel ◽  
Helix Bundle ◽  
Four Helix Bundle

scholarly journals An arginine tetrad as mediator of input-dependent and input-independent ATPases in the clock protein KaiC

2014 ◽  
Vol 70 (5) ◽  
pp. 1375-1390 ◽  
Author(s):  
Rekha Pattanayek ◽  
Yao Xu ◽  
Aashish Lamichhane ◽  
Carl H. Johnson ◽  
Martin Egli
Keyword(s):  
Crystal Structure ◽  
Atpase Activity ◽  
Circadian Clock ◽  
Daily Cycle ◽  
Input Signals ◽  
Loop Regions ◽  
Insight Into ◽  
Shed Light ◽  
Clock Protein

A post-translational oscillator (PTO) composed of the proteins KaiA, KaiB and KaiC is at the heart of the cyanobacterial circadian clock. KaiC interacts with KaiA and KaiB over the daily cycle, and CII domains undergo rhythmic phosphorylation/dephosphorylation with a 24 h period. Both the N-terminal (CI) and C-terminal (CII) rings of KaiC exhibit ATPase activity. The CI ATPase proceeds in an input-independent fashion, but the CII ATPase is subject to metabolic input signals. The crystal structure of KaiC fromThermosynechococcus elongatusallows insight into the different anatomies of the CI and CII ATPases. Four consecutive arginines in CI (Arg linker) that connect the P-loop, CI subunits and CI and CII at the ring interface are primary candidates for the coordination of the CI and CII activities. The mutation of linker residues alters the period or triggers arhythmic behavior. Comparison between the CI and CII structures also reveals differences in loop regions that are key to KaiA and KaiB binding and activation of CII ATPase and kinase. Common packing features in KaiC crystals shed light on the KaiB–KaiC interaction.

scholarly journals Correction: Crystal structure of the C-terminal four-helix bundle of the potassium channel KCa3.1

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0205540
Author(s):  
Tianyang Ji ◽  
Senena Corbalán-García ◽  
Stevan R. Hubbard
Keyword(s):  
Crystal Structure ◽  
Potassium Channel ◽  
Helix Bundle ◽  
Four Helix Bundle

scholarly journals Crystal structure of human cytosolic aspartyl-tRNA synthetase

2014 ◽  
Vol 70 (a1) ◽  
pp. C1403-C1403
Author(s):  
Sang Ho Park ◽  
Kyung Rok Kim ◽  
Hyoun Sook Kim ◽  
Kyung Hee Rhee ◽  
Byung-Gyu Kim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Binding Site ◽  
Elongation Factor ◽  
Trna Synthetase ◽  
Post Translational Modification ◽  
Elongation Factor 1Α ◽  
Dimer Interface ◽  
Switching Model ◽  
Cognate Trna

Human cytosolic aspartyl-tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi-tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling pathways. Here, we report the crystal structure of DRS at 2.25 Å resolution. DRS is a homodimer with a dimer interface 3,750.5 Å2which comprises of 16.6% of the monomeric surface area. Our structure reveals the C-terminal end of the N-helix which is considered as a unique addition in DRS, and its conformation further supports the switching model of the N-helix for the transfer of tRNAAsp to elongation factor 1α. From our analyses of the crystal structure and post-translational modification of DRS, we suggest that the phosphorylation of Ser146 provokes the separation of DRS from the MSC and provides the binding site for an interaction partner with unforeseen functions.

scholarly journals Insights into dimerization and four-helix bundle formation found by dissection of the dimer interface of the GrpE protein fromEscherichia coli

2003 ◽  
Vol 12 (6) ◽  
pp. 1205-1215 ◽  
Author(s):  
Andrew F. Mehl ◽  
Luke D. Heskett ◽  
Sumesh S. Jain ◽  
Borries Demeler
Keyword(s):  
Dimer Interface ◽  
Fromescherichia Coli ◽  
Helix Bundle ◽  
Four Helix Bundle
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