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Signaling protein, electron transport PDB id
1jnu
Jmol
Contents
Protein chains
104 a.a. *
Ligands
FMN ×4
Waters ×65
* Residue conservation analysis
PDB id:
1jnu
Name: Signaling protein, electron transport
Title: Photoexcited structure of the plant photoreceptor domain, phy3 lov2
Structure: Phy3 protein. Chain: a, b, c, d. Fragment: fmn-binding domain of chimeric phytochrome/phototropin photoreceptor, lov3. Synonym: phy3 lov2. Engineered: yes. Other_details: contains a cysteinyl-flavin c(4a) covalent adduct
Source: Adiantum capillus-veneris. Organism_taxid: 13818. Gene: phy3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.60Å     R-factor:   0.238     R-free:   0.259
Authors: S.Crosson,K.Moffat
Key ref: S.Crosson and K.Moffat (2002). Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch. Plant Cell, 14, 1067-1075. PubMed id: 12034897 DOI: 10.1105/tpc.010475
Date:
25-Jul-01     Release date:   14-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9ZWQ6  (Q9ZWQ6_ADICA) -  PHY3
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1465 a.a.
104 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   3 terms 
  Biochemical function     two-component sensor activity     1 term  

 

 
DOI no: 10.1105/tpc.010475 Plant Cell 14:1067-1075 (2002)
PubMed id: 12034897  
 
 
Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch.
S.Crosson, K.Moffat.
 
  ABSTRACT  
 
The phototropins are flavoprotein kinases that control phototropic bending, light-induced chloroplast movement, and stomatal opening in plants. Two flavin mononucleotide binding light, oxygen, or voltage (LOV) domains are the sites for initial photochemistry in these blue light photoreceptors. We have determined the steady state, photoexcited crystal structure of a flavin-bound LOV domain. The structure reveals a unique photochemical switch in the flavin binding pocket in which the absorption of light drives the formation of a reversible covalent bond between a highly conserved Cys residue and the flavin cofactor. This provides a molecular picture of a cysteinyl-flavin covalent adduct, the presumed signaling species that leads to phototropin kinase activation and subsequent signal transduction. We identify closely related LOV domains in two eubacterial proteins that suggests the light-induced conformational change evident in this structure is an ancient biomolecular response to light, arising before the appearance of plants.
 

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.  
21261629 I.H.van Stokkum, M.Gauden, S.Crosson, R.van Grondelle, K.Moffat, and J.T.Kennis (2011).
The primary photophysics of the Avena sativa phototropin 1 LOV2 domain observed with time-resolved emission spectroscopy.
  Photochem Photobiol, 87, 534-541.  
21303137 M.Hakala, K.Marushkevich, L.Khriachtchev, K.Hämäläinen, and M.Räsänen (2011).
Experimental and computational study of crystalline formic acid composed of the higher-energy conformer.
  J Chem Phys, 134, 054506.  
21198648 S.Weber, C.Schroeder, S.Kacprzak, T.Mathes, R.M.Kowalczyk, L.O.Essen, P.Hegemann, E.Schleicher, and R.Bittl (2011).
Light-generated paramagnetic intermediates in BLUF domains.
  Photochem Photobiol, 87, 574-583.  
21336931 T.Drepper, U.Krauss, S.Meyer Zu Berstenhorst, J.Pietruszka, and K.E.Jaeger (2011).
Lights on and action! Controlling microbial gene expression by light.
  Appl Microbiol Biotechnol, 90, 23-40.  
21388385 Y.Nakasone, and K.J.Hellingwerf (2011).
On the binding of BODIPY-GTP by the photosensory protein YtvA from the common soil bacterium Bacillus subtilis.
  Photochem Photobiol, 87, 542-547.  
21235644 e.l.-.B.Djouani-Tahri, J.M.Christie, S.Sanchez-Ferandin, F.Sanchez, F.Y.Bouget, and F.Corellou (2011).
A eukaryotic LOV-histidine kinase with circadian clock function in the picoalga Ostreococcus.
  Plant J, 65, 578-588.  
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.  
20562867 D.Strickland, X.Yao, G.Gawlak, M.K.Rosen, K.H.Gardner, and T.R.Sosnick (2010).
Rationally improving LOV domain-based photoswitches.
  Nat Methods, 7, 623-626.  
19915832 D.Tisch, and M.Schmoll (2010).
Light regulation of metabolic pathways in fungi.
  Appl Microbiol Biotechnol, 85, 1259-1277.  
21081920 E.Peter, B.Dick, and S.A.Baeurle (2010).
Mechanism of signal transduction of the LOV2-Jα photosensor from Avena sativa.
  Nat Commun, 1, 122.  
20192732 W.R.Briggs (2010).
A wandering pathway in plant biology: from wildflowers to phototropins to bacterial virulence.
  Annu Rev Plant Biol, 61, 1.  
19836329 A.Möglich, R.A.Ayers, and K.Moffat (2009).
Structure and signaling mechanism of Per-ARNT-Sim domains.
  Structure, 17, 1282-1294.  
19217862 A.Pfeifer, T.Majerus, K.Zikihara, D.Matsuoka, S.Tokutomi, J.Heberle, and T.Kottke (2009).
Time-resolved Fourier transform infrared study on photoadduct formation and secondary structural changes within the phototropin LOV domain.
  Biophys J, 96, 1462-1470.  
19348760 A.Yamamoto, T.Iwata, Y.Sato, D.Matsuoka, S.Tokutomi, and H.Kandori (2009).
Light signal transduction pathway from flavin chromophore to the J alpha helix of Arabidopsis phototropin1.
  Biophys J, 96, 2771-2778.  
19357428 J.J.Holland, D.Roberts, and E.Liscum (2009).
Understanding phototropism: from Darwin to today.
  J Exp Bot, 60, 1969-1978.  
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
19581299 M.Avila-Pérez, J.Vreede, Y.Tang, O.Bende, A.Losi, W.Gärtner, and K.Hellingwerf (2009).
In vivo mutational analysis of YtvA from Bacillus subtilis: mechanism of light activation of the general stress response.
  J Biol Chem, 284, 24958-24964.  
19224924 M.Grininger, H.Staudt, P.Johansson, J.Wachtveitl, and D.Oesterhelt (2009).
Dodecin is the key player in flavin homeostasis of archaea.
  J Biol Chem, 284, 13068-13076.
PDB codes: 2vx9 2vxa
19580761 M.T.Alexandre, R.van Grondelle, K.J.Hellingwerf, and J.T.Kennis (2009).
Conformational heterogeneity and propagation of structural changes in the LOV2/Jalpha domain from Avena sativa phototropin 1 as recorded by temperature-dependent FTIR spectroscopy.
  Biophys J, 97, 238-247.  
19580760 M.T.Alexandre, T.Domratcheva, C.Bonetti, L.J.van Wilderen, R.van Grondelle, M.L.Groot, K.J.Hellingwerf, and J.T.Kennis (2009).
Primary reactions of the LOV2 domain of phototropin studied with ultrafast mid-infrared spectroscopy and quantum chemistry.
  Biophys J, 97, 227-237.  
19243237 T.Senda, M.Senda, S.Kimura, and T.Ishida (2009).
Redox control of protein conformation in flavoproteins.
  Antioxid Redox Signal, 11, 1741-1766.  
19271777 U.E.Ukaegbu, and A.C.Rosenzweig (2009).
Structure of the redox sensor domain of Methylococcus capsulatus (Bath) MmoS.
  Biochemistry, 48, 2207-2215.
PDB code: 3ewk
19063612 A.I.Nash, W.H.Ko, S.M.Harper, and K.H.Gardner (2008).
A conserved glutamine plays a central role in LOV domain signal transmission and its duration.
  Biochemistry, 47, 13842-13849.  
  19704767 M.A.Jones, and J.M.Christie (2008).
Phototropin receptor kinase activation by blue light.
  Plant Signal Behav, 3, 44-46.  
18989482 M.T.Alexandre, R.van Grondelle, K.J.Hellingwerf, B.Robert, and J.T.Kennis (2008).
Perturbation of the ground-state electronic structure of FMN by the conserved cysteine in phototropin LOV2 domains.
  Phys Chem Chem Phys, 10, 6693-6702.  
18444900 P.Hegemann (2008).
Algal sensory photoreceptors.
  Annu Rev Plant Biol, 59, 167-189.  
18604833 R.J.Kutta, E.S.Hofinger, H.Preuss, G.Bernhardt, and B.Dick (2008).
Blue-light induced interaction of LOV domains from Chlamydomonas reinhardtii.
  Chembiochem, 9, 1931-1938.  
18604202 X.Yao, M.K.Rosen, and K.H.Gardner (2008).
Estimation of the available free energy in a LOV2-J alpha photoswitch.
  Nat Chem Biol, 4, 491-497.  
18028200 A.Losi (2007).
Flavin-based Blue-Light photosensors: a photobiophysics update.
  Photochem Photobiol, 83, 1283-1300.  
17764689 A.Möglich, and K.Moffat (2007).
Structural basis for light-dependent signaling in the dimeric LOV domain of the photosensor YtvA.
  J Mol Biol, 373, 112-126.
PDB codes: 2pr5 2pr6
17986614 E.B.Purcell, D.Siegal-Gaskins, D.C.Rawling, A.Fiebig, and S.Crosson (2007).
A photosensory two-component system regulates bacterial cell attachment.
  Proc Natl Acad Sci U S A, 104, 18241-18246.  
17990262 G.Nöll, G.Hauska, P.Hegemann, K.Lanzl, T.Nöll, M.von Sanden-Flohe, and B.Dick (2007).
Redox properties of LOV domains: chemical versus photochemical reduction, and influence on the photocycle.
  Chembiochem, 8, 2256-2264.  
17067285 J.M.Christie (2007).
Phototropin blue-light receptors.
  Annu Rev Plant Biol, 58, 21-45.  
17487311 M.A.van der Horst, J.C.Arents, R.Kort, and K.J.Hellingwerf (2007).
Binding, tuning and mechanical function of the 4-hydroxy-cinnamic acid chromophore in photoactive yellow protein.
  Photochem Photobiol Sci, 6, 571-579.  
17200735 V.Buttani, A.Losi, T.Eggert, U.Krauss, K.E.Jaeger, Z.Cao, and W.Gärtner (2007).
Conformational analysis of the blue-light sensing protein YtvA reveals a competitive interface for LOV-LOV dimerization and interdomain interactions.
  Photochem Photobiol Sci, 6, 41-49.  
17443319 V.Buttani, W.Gärtner, and A.Losi (2007).
NTP-binding properties of the blue-light receptor YtvA and effects of the E105L mutation.
  Eur Biophys J, 36, 831-839.  
17944933 W.Eisenreich, M.Joshi, B.Illarionov, G.Richter, W.Römisch-Margl, F.Müller, A.Bacher, and M.Fischer (2007).
13C Isotopologue editing of FMN bound to phototropin domains.
  FEBS J, 274, 5876-5890.  
17380429 W.R.Briggs (2007).
The LOV domain: a chromophore module servicing multiple photoreceptors.
  J Biomed Sci, 14, 499-504.  
16879651 F.Silva, S.Torres-Martínez, and V.Garre (2006).
Distinct white collar-1 genes control specific light responses in Mucor circinelloides.
  Mol Microbiol, 61, 1023-1037.  
16935961 P.L.Freddolino, M.Dittrich, and K.Schulten (2006).
Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins.
  Biophys J, 91, 3630-3639.  
16922605 R.Narikawa, K.Zikihara, K.Okajima, Y.Ochiai, M.Katayama, Y.Shichida, S.Tokutomi, and M.Ikeuchi (2006).
Three putative photosensory light, oxygen or voltage (LOV) domains with distinct biochemical properties from the filamentous cyanobacterium Anabaena sp. PCC 7120.
  Photochem Photobiol, 82, 1627-1633.  
16923906 T.A.Gaidenko, T.J.Kim, A.L.Weigel, M.S.Brody, and C.W.Price (2006).
The blue-light receptor YtvA acts in the environmental stress signaling pathway of Bacillus subtilis.
  J Bacteriol, 188, 6387-6395.  
16552739 T.Kottke, P.Hegemann, B.Dick, and J.Heberle (2006).
The photochemistry of the light-, oxygen-, and voltage-sensitive domains in the algal blue light receptor phot.
  Biopolymers, 82, 373-378.  
16679373 Y.Nakasone, T.Eitoku, D.Matsuoka, S.Tokutomi, and M.Terazima (2006).
Kinetic measurement of transient dimerization and dissociation reactions of Arabidopsis phototropin 1 LOV2 domain.
  Biophys J, 91, 645-653.  
16022561 A.Losi, E.Ghiraldelli, S.Jansen, and W.Gärtner (2005).
Mutational effects on protein structural changes and interdomain interactions in the blue-light sensing LOV protein YtvA.
  Photochem Photobiol, 81, 1145-1152.  
16129597 D.Bourgeois, and A.Royant (2005).
Advances in kinetic protein crystallography.
  Curr Opin Struct Biol, 15, 538-547.  
16150710 D.Matsuoka, and S.Tokutomi (2005).
Blue light-regulated molecular switch of Ser/Thr kinase in phototropin.
  Proc Natl Acad Sci U S A, 102, 13337-13342.  
15469384 E.Knieb, M.Salomon, and W.Rüdiger (2005).
Autophosphorylation, electrophoretic mobility and immunoreaction of oat phototropin 1 under UV and blue Light.
  Photochem Photobiol, 81, 177-182.  
15879473 H.Guo, T.Kottke, P.Hegemann, and B.Dick (2005).
The phot LOV2 domain and its interaction with LOV1.
  Biophys J, 89, 402-412.  
16121278 M.A.van der Horst, W.Laan, S.Yeremenko, A.Wende, P.Palm, D.Oesterhelt, and K.J.Hellingwerf (2005).
From primary photochemistry to biological function in the blue-light photoreceptors PYP and AppA.
  Photochem Photobiol Sci, 4, 688-693.  
16852614 M.Dittrich, P.L.Freddolino, and K.Schulten (2005).
When light falls in LOV: a quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii.
  J Phys Chem B, 109, 13006-13013.  
16287715 Q.He, and Y.Liu (2005).
Molecular mechanism of light responses in Neurospora: from light-induced transcription to photoadaptation.
  Genes Dev, 19, 2888-2899.  
15924418 S.Anderson, V.Dragnea, S.Masuda, J.Ybe, K.Moffat, and C.Bauer (2005).
Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides.
  Biochemistry, 44, 7998-8005.
PDB code: 1yrx
16189596 U.Krauss, A.Losi, W.Gärtner, K.E.Jaeger, and T.Eggert (2005).
Initial characterization of a blue-light sensing, phototropin-related protein from Pseudomonas putida: a paradigm for an extended LOV construct.
  Phys Chem Chem Phys, 7, 2804-2811.  
15548612 A.J.Fischer, and J.C.Lagarias (2004).
Harnessing phytochrome's glowing potential.
  Proc Natl Acad Sci U S A, 101, 17334-17339.  
15339223 A.Losi, E.Ternelli, and W.Gärtner (2004).
Tryptophan fluorescence in the Bacillus subtilis phototropin-related protein YtvA as a marker of interdomain interaction.
  Photochem Photobiol, 80, 150-153.  
14747340 A.Losi, T.Kottke, and P.Hegemann (2004).
Recording of blue light-induced energy and volume changes within the wild-type and mutated phot-LOV1 domain from Chlamydomonas reinhardtii.
  Biophys J, 86, 1051-1060.  
15568974 A.R.Grossman, M.Lohr, and C.S.Im (2004).
Chlamydomonas reinhardtii in the landscape of pigments.
  Annu Rev Genet, 38, 119-173.  
15299148 C.A.Brautigam, B.S.Smith, Z.Ma, M.Palnitkar, D.R.Tomchick, M.Machius, and J.Deisenhofer (2004).
Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana.
  Proc Natl Acad Sci U S A, 101, 12142-12147.
PDB codes: 1u3c 1u3d
15568973 M.Chen, J.Chory, and C.Fankhauser (2004).
Light signal transduction in higher plants.
  Annu Rev Genet, 38, 87.  
15009198 M.H.Hefti, K.J.Françoijs, S.C.de Vries, R.Dixon, and J.Vervoort (2004).
The PAS fold. A redefinition of the PAS domain based upon structural prediction.
  Eur J Biochem, 271, 1198-1208.  
15274923 S.Anderson, V.Srajer, R.Pahl, S.Rajagopal, F.Schotte, P.Anfinrud, M.Wulff, and K.Moffat (2004).
Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein.
  Structure, 12, 1039-1045.
PDB codes: 1s1y 1s1z
12856890 C.Neiss, and P.Saalfrank (2003).
Ab initio quantum chemical investigation of the first steps of the photocycle of phototropin: a model study.
  Photochem Photobiol, 77, 101-109.  
12970196 C.Schwerdtfeger, and H.Linden (2003).
VIVID is a flavoprotein and serves as a fungal blue light photoreceptor for photoadaptation.
  EMBO J, 22, 4846-4855.  
12524299 K.Ataka, P.Hegemann, and J.Heberle (2003).
Vibrational spectroscopy of an algal Phot-LOV1 domain probes the molecular changes associated with blue-light reception.
  Biophys J, 84, 466-474.  
12719523 P.Cheng, Q.He, Y.Yang, L.Wang, and Y.Liu (2003).
Functional conservation of light, oxygen, or voltage domains in light sensing.
  Proc Natl Acad Sci U S A, 100, 5938-5943.  
12547798 T.Kottke, J.Heberle, D.Hehn, B.Dick, and P.Hegemann (2003).
Phot-LOV1: photocycle of a blue-light receptor domain from the green alga Chlamydomonas reinhardtii.
  Biophys J, 84, 1192-1201.  
14556317 W.Laan, M.A.van der Horst, I.H.van Stokkum, and K.J.Hellingwerf (2003).
Initial characterization of the primary photochemistry of AppA, a blue-light-using flavin adenine dinucleotide-domain containing transcriptional antirepressor protein from Rhodobacter sphaeroides: a key role for reversible intramolecular proton transfer from the flavin adenine dinucleotide chromophore to a conserved tyrosine?
  Photochem Photobiol, 78, 290-297.  
12383086 J.M.Christie, T.E.Swartz, R.A.Bogomolni, and W.R.Briggs (2002).
Phototropin LOV domains exhibit distinct roles in regulating photoreceptor function.
  Plant J, 32, 205-219.  
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 code is shown on the right.