PDBsum entry 2z6c

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Transferase PDB id
Protein chains
121 a.a. *
FMN ×2
Waters ×140
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of lov1 domain of phototropin1 from arabidopsis thaliana
Structure: Phototropin-1. Chain: a, b. Fragment: unp residues 180-308, lov1 domain. Synonym: non-phototropic hypocotyl protein 1, root phototropism protein 1. Engineered: yes
Source: Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Gene: phot1, jk224, nph1, rpt1. Expressed in: escherichia coli. Expression_system_taxid: 562
2.10Å     R-factor:   0.192     R-free:   0.243
Authors: M.Nakasako,D.Matsuoka,S.Tokutomi
Key ref:
M.Nakasako et al. (2008). Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2. J Mol Biol, 381, 718-733. PubMed id: 18585389 DOI: 10.1016/j.jmb.2008.06.033
29-Jul-07     Release date:   29-Jul-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O48963  (PHOT1_ARATH) -  Phototropin-1
996 a.a.
121 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Non-specific serine/threonine protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
+ protein
Bound ligand (Het Group name = FMN)
matches with 61.00% similarity
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   2 terms 
  Biochemical function     signal transducer activity     2 terms  


DOI no: 10.1016/j.jmb.2008.06.033 J Mol Biol 381:718-733 (2008)
PubMed id: 18585389  
Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2.
M.Nakasako, K.Zikihara, D.Matsuoka, H.Katsura, S.Tokutomi.
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.
  Selected figure(s)  
Figure 1.
Fig. 1. (a) A schematic illustration of domain organization in phot1 and phot2. P1L1 and P2L1 used in this study are indicated by solid lines. (b) A sequence alignment of six LOV domains and three PAS domains, the structures of which are known. The LOV domains are Arabidopsis P1L1 (AtP1L1; residues Gly180-Lys329), Arabidopsis P2L1 (AtP2L1; residues Phe117-Lys265), C. reinhardtii phot-LOV1 (CrPL1; residues Gly17-Ser125; PDB accession code 1N9L),^22 Ad. capillus veneris phy3-LOV2 (AdP3L2; residues Lys929-Met1032; 1G28),^14 A. sativa phot1-LOV2 (AsP1L2; residues Met36-Glu184; 2PD7),^24 and Neurospora crassa Vivid (NcVivid; residues Met401-Leu546; 2V0U).^41 The PAS domains are human ARNT PAS-B (HmARNT; residues Cys358-Lys465; 2A24),^38 human HIF-2α PAS-B (HmHIF2a; residues Lys242-Glu348; 2A24),^38 and the full-length H-NOXA-like domain of STHK from Nostoc punctiforme (NpSTHK; residues Met1-Ile107; 2P04).^39 Additionally shown sequences are those of Arabidopsis phot2-LOV2 (AtP2L2; residues Asp366-Arg506)^29 and the H-NOXA domain of rat sGC β1 (RtsGCb1; residues Asn201-Leu333),^40 which has a sequence homologous to the domain of STHK. The symbol ‘ angle bracket angle bracket ’ in sGCβ1 indicates insertion of 19 residues. Residues with pink background form α-helices, and those with green background form β strands. The yellow background in P1L1 and P2L1 indicates that the residues are invisible in electron density maps. The conserved cysteine residues for FMN binding among LOV domains are indicated by a green box. The cyan and red arrows indicate the residues that are important for subunit associations of P1L1 and P2L1, respectively. The residues with green arrows are engaged in hydrophobic interactions between the A′α helix and the β-scaffold in P1L1 or P2L1 (see also Fig. 2 and Fig. 3). Names of secondary structures (A′α–Jα) are labeled according to the manner proposed.^[14]^ and ^[24] The residues with solid underlines contribute to interactions in the ARNT–HIF-2α PAS-B complex proposed by a nuclear magnetic resonance study.^38 The purple boxes indicate structurally and/or biochemically identified residues that are necessary for the dimeric associations of the PAS-B complex, the H-NOXA-like domain of STHK,^39 or the H-NOXA domain of sGC.^39 The alignment of sequences for structure-known domains was carried out manually by viewing the structures superimposed onto chain A of P1L1.
Figure 2.
Fig. 2. Stereoplots schematically illustrating the structures of P1L1 (a) and P2L1 (b) dimers. Structures of subunits are shown as ribbon models, with cofactor FMN molecules presented as element-colored ball-and-stick models. Side chains of residues engaged in intersubunit interactions are shown by the ball-and-stick models or spheres. The residues are Asn259 (gray stick model) and disulfide-forming Cys261 (green spheres) in P1L1; and Thr215 (pink stick), Thr217 (yellow spheres), Ile219 (orange sticks), and Mer232 (cyan sticks) in P2L1. Red spheres indicate the positions of hydration water molecules assisting intersubunit interactions. Names of some secondary structures are labeled (see also Fig. 1b). (c) A stereoplot demonstrating the difference in the subunit associations between P1L1 and P2L1 dimers. The structural models are shown as tube traces of C^α atoms and are colored as in (a) and (b). For clarity, the A′α helix is omitted in the blue subunit of P1L1. P1L1 and P2L1 are superimposed such that the subunits with A′α lying on the subunit interface overlap optimally in their Aβ, Gβ, Hβ, and Iβ strands. The dotted red lines demonstrate how the molecular axes of the rest of the subunits differ between P1L1 and P2L1. The pseudo 2-fold rotational symmetry axis in the P1L1 dimer is shown by a dashed line.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 718-733) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21352235 A.Losi, and W.Gärtner (2011).
Old chromophores, new photoactivation paradigms, trendy applications: flavins in blue light-sensing photoreceptors.
  Photochem Photobiol, 87, 491-510.  
20192744 A.Möglich, X.Yang, R.A.Ayers, and K.Moffat (2010).
Structure and function of plant photoreceptors.
  Annu Rev Plant Biol, 61, 21-47.  
20062844 Y.Tang, Z.Cao, E.Livoti, U.Krauss, K.E.Jaeger, W.Gärtner, and A.Losi (2010).
Interdomain signalling in the blue-light sensing and GTP-binding protein YtvA: a mutagenesis study uncovering the importance of specific protein sites.
  Photochem Photobiol Sci, 9, 47-56.  
19836329 A.Möglich, R.A.Ayers, and K.Moffat (2009).
Structure and signaling mechanism of Per-ARNT-Sim domains.
  Structure, 17, 1282-1294.  
19718042 B.D.Zoltowski, B.Vaccaro, and B.R.Crane (2009).
Mechanism-based tuning of a LOV domain photoreceptor.
  Nat Chem Biol, 5, 827-834.
PDB codes: 3hji 3hjk
18930433 E.Demarsy, and C.Fankhauser (2009).
Higher plants use LOV to perceive blue light.
  Curr Opin Plant Biol, 12, 69-74.  
19712683 J.S.Lamb, B.D.Zoltowski, S.A.Pabit, L.Li, B.R.Crane, and L.Pollack (2009).
Illuminating solution responses of a LOV domain protein with photocoupled small-angle X-ray scattering.
  J Mol Biol, 393, 909-919.
PDB code: 3is2
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.