3K09

Crystal structure of the phosphorylation-site mutant S431D of the KaiC circadian clock protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structures of KaiC Circadian Clock Mutant Proteins: A New Phosphorylation Site at T426 and Mechanisms of Kinase, ATPase and Phosphatase.

Pattanayek, R.Mori, T.Xu, Y.Pattanayek, S.Johnson, C.H.Egli, M.

(2009) PLoS One 4: e7529-e7529

  • DOI: https://doi.org/10.1371/journal.pone.0007529
  • Primary Citation of Related Structures:  
    3JZM, 3K09, 3K0A, 3K0C, 3K0E, 3K0F

  • PubMed Abstract: 

    The circadian clock of the cyanobacterium Synechococcus elongatus can be reconstituted in vitro by three proteins, KaiA, KaiB and KaiC. Homo-hexameric KaiC displays kinase, phosphatase and ATPase activities; KaiA enhances KaiC phosphorylation and KaiB antagonizes KaiA. Phosphorylation and dephosphorylation of the two known sites in the C-terminal half of KaiC subunits, T432 and S431, follow a strict order (TS-->pTS-->pTpS-->TpS-->TS) over the daily cycle, the origin of which is not understood. To address this void and to analyze the roles of KaiC active site residues, in particular T426, we determined structures of single and double P-site mutants of S. elongatus KaiC.


  • Organizational Affiliation

    Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Circadian clock protein kinase kaiC
A, B, E
519Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 1 
Gene Names: kaicsee0011Synpcc7942_1216
EC: 2.7.11.1
UniProt
Find proteins for Q79PF4 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q79PF4 
Go to UniProtKB:  Q79PF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79PF4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Circadian clock protein kinase kaiC
C, D, F
519Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 1 
Gene Names: kaicsee0011Synpcc7942_1216
EC: 2.7.11.1
UniProt
Find proteins for Q79PF4 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q79PF4 
Go to UniProtKB:  Q79PF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79PF4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth D]
FA [auth E]
GA [auth E]
K [auth A]
KA [auth F]
AA [auth D],
FA [auth E],
GA [auth E],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
Z [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth E]
G [auth A]
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
G [auth A],
H [auth A],
HA [auth F],
I [auth A],
IA [auth F],
J [auth A],
JA [auth F],
M [auth A],
N [auth B],
Q [auth C],
R [auth C],
S [auth C],
V [auth C],
W [auth D],
X [auth D],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B, E
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.5α = 90
b = 135.83β = 90
c = 204.32γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description