2ZFW

Crystal structure of Pex from Synechococcus sp. (strain PCC 7942) (Anacystis nidulans R2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Functionally important structural elements of the cyanobacterial clock-related protein Pex.

Kurosawa, S.Murakami, R.Onai, K.Morishita, M.Hasegawa, D.Iwase, R.Uzumaki, T.Hayashi, F.Kitajima-Ihara, T.Sakata, S.Murakami, M.Kouyama, T.Ishiura, M.

(2009) Genes Cells 14: 1-16

  • DOI: 10.1111/j.1365-2443.2008.01245.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pex, a clock-related protein involved in the input pathway of the cyanobacterial circadian clock system, suppresses the expression of clock gene kaiA and lengthens the circadian period. Here, we determined the crystal structure of Anabaena Pex (AnaPe ...

    Pex, a clock-related protein involved in the input pathway of the cyanobacterial circadian clock system, suppresses the expression of clock gene kaiA and lengthens the circadian period. Here, we determined the crystal structure of Anabaena Pex (AnaPex; Anabaena sp. strain PCC 7120) and Synechococcus Pex (SynPex; Synechococcus sp. strain PCC 7942). Pex is a homodimer that forms a winged-helix structure. Using the DNase I protection and electrophoresis mobility shift assays on a Synechococcus kaiA upstream region, we identified a minimal 25-bp sequence that contained an imperfectly inverted repeat sequence as the Pex-binding sequence. Based on crystal structure, we predicted the amino acid residues essential for Pex's DNA-binding activity and examined the effects of various Ala-substitutions in the alpha3 helix and wing region of Pex on in vitro DNA-binding activity and in vivo rhythm functions. Mutant AnaPex proteins carrying a substitution in the wing region displayed no specific DNA-binding activity, whereas those carrying a substitution in the alpha3 helix did display specific binding activity. But the latter were less thermostable than wild-type AnaPex and their in vitro functions were defective. We concluded that Pex binds a kaiA upstream DNA sequence via its wing region and that its alpha3 helix is probably important to its stability.


    Organizational Affiliation

    Department of Physics, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pex
A, B, D, E
148Synechococcus elongatus (strain PCC 7942)Mutation(s): 0 
Gene Names: pex
Find proteins for O66226 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  O66226
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.240 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 117.978α = 90.00
b = 117.978β = 90.00
c = 92.210γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
CNSphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-01-14 
  • Released Date: 2009-01-20 
  • Deposition Author(s): Kouyama, T.

Revision History 

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance