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PDBsum entry 2pd7

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protein ligands Protein-protein interface(s) links
Circadian clock protein PDB id
2pd7
Jmol
Contents
Protein chains
149 a.a. *
Ligands
FAD ×2
Waters ×313
* Residue conservation analysis
PDB id:
2pd7
Name: Circadian clock protein
Title: 2.0 angstrom crystal structure of the fungal blue-light photoreceptor vivid
Structure: Vivid pas protein vvd. Chain: a, b. Fragment: residues 37-184. Synonym: hypothetical protein ncu03967.1. Engineered: yes
Source: Neurospora crassa. Organism_taxid: 5141. Gene: vvd, g17a4.050. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.00Å     R-factor:   0.245     R-free:   0.285
Authors: B.D.Zoltowski,B.R.Crane,A.M.Bilwes
Key ref:
B.D.Zoltowski et al. (2007). Conformational switching in the fungal light sensor Vivid. Science, 316, 1054-1057. PubMed id: 17510367 DOI: 10.1126/science.1137128
Date:
31-Mar-07     Release date:   05-Jun-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9C3Y6  (Q9C3Y6_NEUCS) -  Vivid PAS protein VVD
Seq:
Struc:
186 a.a.
149 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   1 term 
  Biochemical function     signal transducer activity     1 term  

 

 
DOI no: 10.1126/science.1137128 Science 316:1054-1057 (2007)
PubMed id: 17510367  
 
 
Conformational switching in the fungal light sensor Vivid.
B.D.Zoltowski, C.Schwerdtfeger, J.Widom, J.J.Loros, A.M.Bilwes, J.C.Dunlap, B.R.Crane.
 
  ABSTRACT  
 
The Neurospora crassa photoreceptor Vivid tunes blue-light responses and modulates gating of the circadian clock. Crystal structures of dark-state and light-state Vivid reveal a light, oxygen, or voltage Per-Arnt-Sim domain with an unusual N-terminal cap region and a loop insertion that accommodates the flavin cofactor. Photoinduced formation of a cystein-flavin adduct drives flavin protonation to induce an N-terminal conformational change. A cysteine-to-serine substitution remote from the flavin adenine dinucleotide binding site decouples conformational switching from the flavin photocycle and prevents Vivid from sending signals in Neurospora. Key elements of this activation mechanism are conserved by other photosensors such as White Collar-1, ZEITLUPE, ENVOY, and flavin-binding, kelch repeat, F-BOX 1 (FKF1).
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. VVD structure. (A) Crystallographic dimer of VVD-36, including the PAS core (blue), N-terminal cap (yellow), and FAD insertion loop (red). The N terminus, resolved only in the left molecule, projects toward the solvent-exposed FAD adenosine moiety (orange). (B) Superposition of the PAS domains of VVD (green), PYP (magenta), Drosophila PER (red), and AsLOV2 domain (blue). All proteins share a structurally conserved PAS ß scaffold (yellow) and helical regions (gray) that pack with a variable helical element possibly involved in signal transduction. (C) Photocycle of VVD-36 at 25°C. Blue-light illumination of VVD forms a photoadduct between Cys^108 and the C4a position of the flavin ring (inset). Adduct formation bleaches the flavin absorption bands at 428, 450, and 478 nm and produces a single peak at 390 nm. Recovery proceeds with t[1/2] = 10^4 s and three isosbestic points at 330, 385, and 413 nm. Spectra are displayed at 3000 s increments.
Figure 2.
Fig. 2. The VVD light state in crystals. (A) Superposition of VVD (yellow) and Adiantum phy3-LOV2 (1G28, blue-gray) active centers show differences in residue composition beneath the flavin [1.5 (aqua) and 3.0 (purple), 2F[obs] – F[calc] electron density]. An alternate conformation of Cys^108 contacts conserved Cys^76 [3.0 (green), F[obs] – F[calc] electron density]. (B) Structural differences in the light state of VVD. Difference electron density reveals covalent bond formation between Cys^108 and flavin C4a and flipping of the Gln^182 amide in response to N5 protonation. F[obs] – F[calc] electron density [2.0 (aqua), 3.0 (blue), –2.0 (orange), and –3.0 (red)], with F[calc] calculated from a model refined with 100% of the dark-state conformation. (C) Expanded view of the structural changes propagating from Gln^182 to a and bß in the VVD-36 light state. Pro^66 undergoes the largest shift (2.0 Å) in the light state (yellow) versus the dark state (orange). Hydrogen bonds (dashed lines) are shown for d < 3.2 Å; except for Cys^71-to-Asp^68 amide, where d = 3.9 Å. Other key contacts are shown in blue. (D) The hinge region between the PAS core and bß. In the light state, Gln^182 rotates to improve interactions between the Gln^182 amide and the Ala^72 carbonyl, Cys^71 swivels to hydrogen-bond with the Asp^68 amide nitrogen, and bß shifts 2 Å. F[obs] – F[calc] omit electron density [1.5 (aqua) and 3.0 (purple)] calculated with bß absent from the model.
 
  The above figures are reprinted by permission from the AAAs: Science (2007, 316, 1054-1057) copyright 2007.  
  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.  
21204917 D.E.Rangel, E.K.Fernandes, G.U.Braga, and D.W.Roberts (2011).
Visible light during mycelial growth and conidiation of Metarhizium robertsii produces conidia with increased stress tolerance.
  FEMS Microbiol Lett, 315, 81-86.  
21028987 D.F.Becker, W.Zhu, and M.A.Moxley (2011).
Flavin redox switching of protein functions.
  Antioxid Redox Signal, 14, 1079-1091.  
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.  
21822294 J.Herrou, and S.Crosson (2011).
Function, structure and mechanism of bacterial photosensory LOV proteins.
  Nat Rev Microbiol, 9, 713-723.  
21245039 N.Hao, M.L.Whitelaw, K.E.Shearwin, I.B.Dodd, and A.Chapman-Smith (2011).
Identification of residues in the N-terminal PAS domains important for dimerization of Arnt and AhR.
  Nucleic Acids Res, 39, 3695-3709.  
21187431 N.Ozturk, C.P.Selby, Y.Annayev, D.Zhong, and A.Sancar (2011).
Reaction mechanism of Drosophila cryptochrome.
  Proc Natl Acad Sci U S A, 108, 516-521.  
20889915 A.F.Philip, M.Kumauchi, and W.D.Hoff (2010).
Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain.
  Proc Natl Acad Sci U S A, 107, 17986-17991.  
20545849 A.J.Campbell, K.J.Watts, M.S.Johnson, and B.L.Taylor (2010).
Gain-of-function mutations cluster in distinct regions associated with the signalling pathway in the PAS domain of the aerotaxis receptor, Aer.
  Mol Microbiol, 77, 575-586.  
20835487 A.Möglich, and K.Moffat (2010).
Engineered photoreceptors as novel optogenetic tools.
  Photochem Photobiol Sci, 9, 1286-1300.  
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.  
20733070 C.H.Chen, B.S.DeMay, A.S.Gladfelter, J.C.Dunlap, and J.J.Loros (2010).
Physical interaction between VIVID and white collar complex regulates photoadaptation in Neurospora.
  Proc Natl Acad Sci U S A, 107, 16715-16720.  
20813262 E.Malzahn, S.Ciprianidis, K.Káldi, T.Schafmeier, and M.Brunner (2010).
Photoadaptation in Neurospora by competitive interaction of activating and inhibitory LOV domains.
  Cell, 142, 762-772.  
19906177 P.Slavny, R.Little, P.Salinas, T.A.Clarke, and R.Dixon (2010).
Quaternary structure changes in a second Per-Arnt-Sim domain mediate intramolecular redox signal relay in the NifL regulatory protein.
  Mol Microbiol, 75, 61-75.  
20807745 S.M.Hunt, S.Thompson, M.Elvin, and C.Heintzen (2010).
VIVID interacts with the WHITE COLLAR complex and FREQUENCY-interacting RNA helicase to alter light and clock responses in Neurospora.
  Proc Natl Acad Sci U S A, 107, 16709-16714.  
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.  
19508644 A.K.Hendrischk, J.Moldt, S.W.Frühwirth, and G.Klug (2009).
Characterization of an unusual LOV domain protein in the alpha-proteobacterium Rhodobacter sphaeroides.
  Photochem Photobiol, 85, 1254-1259.  
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
  19907715 C.H.Chen, and J.J.Loros (2009).
Neurospora sees the light: Light signaling components in a model system.
  Commun Integr Biol, 2, 448-451.  
19380729 C.Sanz, J.Rodríguez-Romero, A.Idnurm, J.M.Christie, J.Heitman, L.M.Corrochano, and A.P.Eslava (2009).
Phycomyces MADB interacts with MADA to form the primary photoreceptor complex for fungal phototropism.
  Proc Natl Acad Sci U S A, 106, 7095-7100.  
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
19221587 K.Chen, and L.Kurgan (2009).
Investigation of atomic level patterns in protein--small ligand interactions.
  PLoS ONE, 4, e4473.  
19139144 K.Schneider, S.Perrino, K.Oelhafen, S.Li, A.Zatsepin, P.Lakin-Thomas, and S.Brody (2009).
Rhythmic conidiation in constant light in vivid mutants of Neurospora crassa.
  Genetics, 181, 917-931.  
19196990 M.R.Evans, P.B.Card, and K.H.Gardner (2009).
ARNT PAS-B has a fragile native state structure with an alternative beta-sheet register nearby in sequence space.
  Proc Natl Acad Sci U S A, 106, 2617-2622.
PDB code: 2k7s
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.  
19402751 S.Hennig, H.M.Strauss, K.Vanselow, O.Yildiz, S.Schulze, J.Arens, A.Kramer, and E.Wolf (2009).
Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2.
  PLoS Biol, 7, e94.
PDB codes: 3gdi 3gec
19836334 S.Yamada, H.Sugimoto, M.Kobayashi, A.Ohno, H.Nakamura, and Y.Shiro (2009).
Structure of PAS-linked histidine kinase and the response regulator complex.
  Structure, 17, 1333-1344.
PDB codes: 3a0r 3a0s 3a0t 3a0u 3a0v 3a0w 3a0x 3a0y 3a0z 3a10
19243237 T.Senda, M.Senda, S.Kimura, and T.Ishida (2009).
Redox control of protein conformation in flavoproteins.
  Antioxid Redox Signal, 11, 1741-1766.  
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.  
18553928 B.D.Zoltowski, and B.R.Crane (2008).
Light activation of the LOV protein vivid generates a rapidly exchanging dimer.
  Biochemistry, 47, 7012-7019.
PDB code: 3d72
18667691 D.Strickland, K.Moffat, and T.R.Sosnick (2008).
Light-activated DNA binding in a designed allosteric protein.
  Proc Natl Acad Sci U S A, 105, 10709-10714.  
19071936 H.Liu, P.Li, J.Zhao, X.Yin, and H.Zhang (2008).
Theoretical investigation on molecular rectification on the basis of asymmetric substitution and proton transfer reaction.
  J Chem Phys, 129, 224704.  
18715002 J.S.Lamb, B.D.Zoltowski, S.A.Pabit, B.R.Crane, and L.Pollack (2008).
Time-resolved dimerization of a PAS-LOV protein measured with photocoupled small angle X-ray scattering.
  J Am Chem Soc, 130, 12226-12227.  
18203838 K.J.Watts, M.S.Johnson, and B.L.Taylor (2008).
Structure-function relationships in the HAMP and proximal signaling domains of the aerotaxis receptor Aer.
  J Bacteriol, 190, 2118-2127.  
18850603 L.Kozma-Bognár, and K.Káldi (2008).
Synchronization of the fungal and the plant circadian clock by light.
  Chembiochem, 9, 2565-2573.  
18202366 L.Navarro-Sampedro, C.Yanofsky, and L.M.Corrochano (2008).
A Genetic Selection For Neurospora crassa Mutants Altered in Their Light Regulation of Transcription.
  Genetics, 178, 171-183.  
  19704767 M.A.Jones, and J.M.Christie (2008).
Phototropin receptor kinase activation by blue light.
  Plant Signal Behav, 3, 44-46.  
18312266 M.Brunner, and K.Káldi (2008).
Interlocked feedback loops of the circadian clock of Neurospora crassa.
  Mol Microbiol, 68, 255-262.  
18820688 M.Etzkorn, H.Kneuper, P.Dünnwald, V.Vijayan, J.Krämer, C.Griesinger, S.Becker, G.Unden, and M.Baldus (2008).
Plasticity of the PAS domain and a potential role for signal transduction in the histidine kinase DcuS.
  Nat Struct Mol Biol, 15, 1031-1039.
PDB code: 2w0n
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
18053205 A.Schuster, C.P.Kubicek, M.A.Friedl, I.S.Druzhinina, and M.Schmoll (2007).
Impact of light on Hypocrea jecorina and the multiple cellular roles of ENVOY in this process.
  BMC Genomics, 8, 449.  
17824925 B.L.Taylor (2007).
Aer on the inside looking out: paradigm for a PAS-HAMP role in sensing oxygen, redox and energy.
  Mol Microbiol, 65, 1415-1424.  
18522516 J.C.Dunlap, J.J.Loros, H.V.Colot, A.Mehra, W.J.Belden, M.Shi, C.I.Hong, L.F.Larrondo, C.L.Baker, C.H.Chen, C.Schwerdtfeger, P.D.Collopy, J.J.Gamsby, and R.Lambreghts (2007).
A circadian clock in Neurospora: how genes and proteins cooperate to produce a sustained, entrainable, and compensated biological oscillator with a period of about a day.
  Cold Spring Harb Symp Quant Biol, 72, 57-68.  
18419278 J.J.Loros, J.C.Dunlap, L.F.Larrondo, M.Shi, W.J.Belden, V.D.Gooch, C.H.Chen, C.L.Baker, A.Mehra, H.V.Colot, C.Schwerdtfeger, R.Lambreghts, P.D.Collopy, J.J.Gamsby, and C.I.Hong (2007).
Circadian output, input, and intracellular oscillators: insights into the circadian systems of single cells.
  Cold Spring Harb Symp Quant Biol, 72, 201-214.  
17872410 M.Sawa, D.A.Nusinow, S.A.Kay, and T.Imaizumi (2007).
FKF1 and GIGANTEA complex formation is required for day-length measurement in Arabidopsis.
  Science, 318, 261-265.  
17671094 S.M.Hunt, M.Elvin, S.K.Crosthwaite, and C.Heintzen (2007).
The PAS/LOV protein VIVID controls temperature compensation of circadian clock phase and development in Neurospora crassa.
  Genes Dev, 21, 1964-1974.  
17576422 W.H.Ko, A.I.Nash, and K.H.Gardner (2007).
A LOVely view of blue light photosensing.
  Nat Chem Biol, 3, 372-374.  
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.