Crystal structure of the circadian clock associated protein Pex from anabaena

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

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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: https://doi.org/10.1111/j.1365-2443.2008.01245.x
  • Primary Citation of Related Structures:  
    2DQL, 2ZFW

  • 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 (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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pex protein
A, B
115Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Find proteins for Q8YQ56 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YQ56 
Go to UniProtKB:  Q8YQ56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YQ56
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PO4

Download Ideal Coordinates CCD File 
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.126α = 90
b = 75.04β = 90
c = 103.705γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-12-21
    Changes: Structure summary
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations