4G86 | pdb_00004g86

Crystal structure of the redox-active cofactor DBMIB bound to the full length circadian clock protein KaiA from Synechococcus elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.265 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Redox-Active Cofactor Dibromothymoquinone Bound to Circadian Clock Protein KaiA and Structural Basis for Dibromothymoquinone's Ability to Prevent Stimulation of KaiC Phosphorylation by KaiA.

Pattanayek, R.Sidiqi, S.K.Egli, M.

(2012) Biochemistry 51: 8050-8052

  • DOI: https://doi.org/10.1021/bi301222t
  • Primary Citation Related Structures: 
    4G86

  • PubMed Abstract: 

    KaiA protein that stimulates KaiC phosphorylation in the cyanobacterial circadian clock was recently shown to be destabilized by dibromothymoquinone (DBMIB), thus revealing KaiA as a sensor of the plastoquinone (PQ) redox state and suggesting an indirect control of the clock by light through PQ redox changes. Here we show using X-ray crystallography that several DBMIBs are bound to KaiA dimer. Some binding modes are consistent with oligomerization of N-terminal KaiA pseudoreceiver domains and/or reduced interdomain flexibility. DBMIB bound to the C-terminal KaiA (C-KaiA) domain and limited stimulation of KaiC kinase activity by C-KaiA in the presence of DBMIB demonstrate that the cofactor may weakly inhibit KaiA-KaiC binding.


  • Organizational Affiliation
    • Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA.

Macromolecule Content 

  • Total Structure Weight: 67.39 kDa 
  • Atom Count: 4,809 
  • Modeled Residue Count: 564 
  • Deposited Residue Count: 568 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Circadian clock protein kaiA
A, B
284Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: kaiAsee0009Synpcc7942_1218
UniProt
Find proteins for Q79PF6 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q79PF6 
Go to UniProtKB:  Q79PF6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79PF6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2PE

Query on 2PE



Download:Ideal Coordinates CCD File
E [auth A]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
BNT

Query on BNT



Download:Ideal Coordinates CCD File
C [auth A],
F [auth A],
G [auth B],
H [auth B]
2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE
C10 H10 Br2 O2
GHHZELQYJPWSMG-UHFFFAOYSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
D [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.265 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.247α = 90
b = 126.354β = 114.36
c = 56.383γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Structure summary