4IJM

Crystal structure of circadian clock protein KaiC A422V mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.352 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Loop-Loop Interactions Regulate KaiA-Stimulated KaiC Phosphorylation in the Cyanobacterial KaiABC Circadian Clock.

Egli, M.Pattanayek, R.Sheehan, J.H.Xu, Y.Mori, T.Smith, J.A.Johnson, C.H.

(2013) Biochemistry 52: 1208-1220

  • DOI: 10.1021/bi301691a

  • PubMed Abstract: 
  • The Synechococcus elongatus KaiA, KaiB, and KaiC proteins in the presence of ATP generate a post-translational oscillator that runs in a temperature-compensated manner with a period of 24 h. KaiA dimer stimulates phosphorylation of KaiC hexamer at tw ...

    The Synechococcus elongatus KaiA, KaiB, and KaiC proteins in the presence of ATP generate a post-translational oscillator that runs in a temperature-compensated manner with a period of 24 h. KaiA dimer stimulates phosphorylation of KaiC hexamer at two sites per subunit, T432 and S431, and KaiB dimers antagonize KaiA action and induce KaiC subunit exchange. Neither the mechanism of KaiA-stimulated KaiC phosphorylation nor that of KaiB-mediated KaiC dephosphorylation is understood in detail at present. We demonstrate here that the A422V KaiC mutant sheds light on the former mechanism. It was previously reported that A422V is less sensitive to dark pulse-induced phase resetting and has a reduced amplitude of the KaiC phosphorylation rhythm in vivo. A422 maps to a loop (422-loop) that continues toward the phosphorylation sites. By pulling on the C-terminal peptide of KaiC (A-loop), KaiA removes restraints from the adjacent 422-loop whose increased flexibility indirectly promotes kinase activity. We found in the crystal structure that A422V KaiC lacks phosphorylation at S431 and exhibits a subtle, local conformational change relative to wild-type KaiC. Molecular dynamics simulations indicate higher mobility of the 422-loop in the absence of the A-loop and mobility differences in other areas associated with phosphorylation activity between wild-type and mutant KaiCs. The A-loop-422-loop relay that informs KaiC phosphorylation sites of KaiA dimer binding propagates to loops from neighboring KaiC subunits, thus providing support for a concerted allosteric mechanism of phosphorylation.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA. martin.egli@vanderbilt.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Circadian clock protein kinase KaiC
A, B, C, D, E, F
512Synechococcus elongatus (strain PCC 7942)Gene Names: kaiC
EC: 2.7.11.1
Find proteins for Q79PF4 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  Q79PF4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
B, C, D, E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, B, C, D, E, F
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.352 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 131.362α = 90.00
b = 134.468β = 90.00
c = 203.936γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
CNSphasing
CNSrefinement
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references