2Z6D

Crystal structure of LOV1 domain of phototropin2 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2

Nakasako, M.Zikihara, K.Matsuoka, D.Katsura, H.Tokutomi, S.

(2008) J Mol Biol 381: 718-733

  • DOI: 10.1016/j.jmb.2008.06.033
  • Primary Citation of Related Structures:  
    2Z6C, 2Z6D

  • PubMed Abstract: 
  • Phototropin (phot) is a blue-light receptor protein that triggers phototropic responses, chloroplast relocation, and stomata opening to maximize the efficiency of photosynthesis in higher plants. Phot is composed of three functional domains. The N-te ...

    Phototropin (phot) is a blue-light receptor protein that triggers phototropic responses, chloroplast relocation, and stomata opening to maximize the efficiency of photosynthesis in higher plants. Phot is composed of three functional domains. The N-terminal half folds into two light-oxygen-voltage-sensing domains called LOV1 and LOV2, each binding a flavin mononucleotide to absorb blue light. The C-terminal half is a serine/threonine kinase domain that causes light-dependent autophosphorylation leading to cellular signaling cascades. LOV2 domain is primarily responsible for activation of the kinase, and LOV1 domain is thought to act as a dimerization site and to regulate sensitivity to activation by blue light. Here we show the crystal structures of LOV1 domains of Arabidopsis phot1 and phot2 in the dark at resolutions of 2.1 A and 2.0 A, respectively. Either LOV1 domain forms a dimer through face-to-face association of beta-scaffolds in the crystallographic asymmetric unit. Three types of interactions stabilizing the dimer structures found are as follows: contacts of side chains in their beta-scaffolds, hydrophobic interactions of a short helix found in the N-terminus of a subunit with the beta-scaffolds of both subunits, and hydrogen bonds mediated by hydration water molecules filling the dimer interface. The critical residues for dimerization are Cys261, forming a disulfide bridge between subunits in phot1-LOV1 domain, and Thr217 and Met232 in phot2-LOV1. The topology in homodimeric associations of the LOV1 domains is discussed when referring to those of homodimers or heterodimers of light-oxygen-voltage-sensing or Per-ARNT-Sim domains. The present results also provide clues to understanding structural basis in dimeric interactions of Per-ARNT-Sim protein modules in cellular signaling.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction analysis of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana
      Nakasako, M., Hirata, M., Shimizu, N., Hosokawa, S., Matsuoka, D., Oka, T., Yamamoto, M., Tokutomi, S.
      (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 617
    • Light-induced structural changes of LOV domain-containing polypeptides from Arabidopsis phototropin 1 and 2 studied by small-angle X-ray scattering
      Nakasako, M., Iwata, T., Matsuoka, D., Tokutomi, S.
      (2004) Biochemistry 43: 14881
    • Quaternary structure of LOV-domain containing polypeptide of Arabidopsis FKF1 protein
      Nakasako, M., Matsuoka, D., Zikihara, K., Tokutomi, S.
      (2005) FEBS Lett 579: 1067

    Organizational Affiliation

    Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522, Japan. nakasako@phys.keio.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phototropin-2AB130Arabidopsis thalianaMutation(s): 0 
Gene Names: PHOT2CAV1KIN7NPL1At5g58140K21L19.6
EC: 2.7.11.1
Find proteins for P93025 (Arabidopsis thaliana)
Explore P93025 
Go to UniProtKB:  P93025
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.52α = 90
b = 66.51β = 92.42
c = 56.69γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance