PDBsum entry 2phy

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Photoreceptor PDB id
Protein chain
125 a.a. *
Waters ×92
* Residue conservation analysis
PDB id:
Name: Photoreceptor
Title: Photoactive yellow protein, dark state (unbleached)
Structure: Photoactive yellow protein. Chain: a. Synonym: pyp
Source: Halorhodospira halophila. Organism_taxid: 1053. Strain: bn9626
1.40Å     R-factor:   0.186     R-free:   0.226
Authors: G.E.O.Borgstahl,E.D.Getzoff
Key ref:
G.E.Borgstahl et al. (1995). 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Biochemistry, 34, 6278-6287. PubMed id: 7756254 DOI: 10.1021/bi00019a004
12-Apr-95     Release date:   15-Oct-95    
Supersedes: 1phy
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P16113  (PYP_HALHA) -  Photoactive yellow protein
125 a.a.
125 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to stimulus   5 terms 
  Biochemical function     signal transducer activity     2 terms  


DOI no: 10.1021/bi00019a004 Biochemistry 34:6278-6287 (1995)
PubMed id: 7756254  
1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore.
G.E.Borgstahl, D.R.Williams, E.D.Getzoff.
A photosensing protein directs light energy captured by its chromophore into a photocycle. The protein's structure must accommodate the photocycle and promote the resulting chemical or conformational changes that lead to signal transduction. The 1.4 A crystallographic structure of photoactive yellow protein, determined by multiple isomorphous replacement methods, provides the first view at atomic resolution of a protein with a photocycle. The alpha/beta fold, which differs from the original chain tracing, shows striking similarity to distinct parts of the signal transduction proteins profilin and the SH2 domain. In the dark state structure of photoactive yellow protein, the novel 4-hydroxycinnamyl chromophore, covalently attached to Cys69, is buried within the major hydrophobic core of the protein and is tethered at both ends by hydrogen bonds. In the active site, the yellow anionic form of the chromophore is stabilized by hydrogen bonds from the side chains of Tyr42 and buried Glu46 to the phenolic oxygen atom and by electrostatic complementarity with the positively charged guanidinium group of Arg52. Thr50 further interlocks Tyr42, Glu46, and Arg52 through a network of active site hydrogen bonds. Arg52, located in a concavity of the protein surface adjacent to the dominant patch of negative electrostatic potential, shields the chromophore from solvent and is positioned to form a gateway for the phototactic signal. Overall, the high-resolution structure of photoactive yellow protein supports a mechanism whereby electrostatic interactions create an active site poised for photon-induced rearrangements and efficient protein-mediated signal transduction.

Literature references that cite this PDB file's key reference

  PubMed id Reference
22338689 M.Schmidt, V.Šrajer, N.Purwar, and S.Tripathi (2012).
The kinetic dose limit in room-temperature time-resolved macromolecular crystallography.
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21301710 C.Loukou, P.Changenet-Barret, M.N.Rager, P.Plaza, M.M.Martin, and J.M.Mallet (2011).
The design, synthesis and photochemical study of a biomimetic cyclodextrin model of photoactive yellow protein (PYP).
  Org Biomol Chem, 9, 2209-2218.  
21822294 J.Herrou, and S.Crosson (2011).
Function, structure and mechanism of bacterial photosensory LOV proteins.
  Nat Rev Microbiol, 9, 713-723.  
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.
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21132197 T.Rocha-Rinza, K.Sneskov, O.Christiansen, U.Ryde, and J.Kongsted (2011).
Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein.
  Phys Chem Chem Phys, 13, 1585-1589.  
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.  
20220103 A.F.Philip, R.A.Nome, G.A.Papadantonakis, N.F.Scherer, and W.D.Hoff (2010).
Spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface.
  Proc Natl Acad Sci U S A, 107, 5821-5826.  
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.  
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.  
20646219 E.Rayko, F.Maumus, U.Maheswari, K.Jabbari, and C.Bowler (2010).
Transcription factor families inferred from genome sequences of photosynthetic stramenopiles.
  New Phytol, 188, 52-66.  
20133754 J.Vreede, J.Juraszek, and P.G.Bolhuis (2010).
Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein.
  Proc Natl Acad Sci U S A, 107, 2397-2402.  
20603670 R.den Heeten, B.K.Muñoz, G.Popa, W.Laan, and P.C.Kamer (2010).
Synthesis of hybrid transition-metalloproteins via thiol-selective covalent anchoring of Rh-phosphine and Ru-phenanthroline complexes.
  Dalton Trans, 39, 8477-8483.  
20432427 W.Laan, B.K.Muñoz, R.den Heeten, and P.C.Kamer (2010).
Artificial metalloenzymes through cysteine-selective conjugation of phosphines to photoactive yellow protein.
  Chembiochem, 11, 1236-1239.  
19836329 A.Möglich, R.A.Ayers, and K.Moffat (2009).
Structure and signaling mechanism of Per-ARNT-Sim domains.
  Structure, 17, 1282-1294.  
  19177345 D.E.Tronrud, and B.W.Matthews (2009).
Sorting the chaff from the wheat at the PDB.
  Protein Sci, 18, 2-5.  
19551213 D.Hoersch, H.Otto, M.A.Cusanovich, and M.P.Heyn (2009).
Time-resolved spectroscopy of dye-labeled photoactive yellow protein suggests a pathway of light-induced structural changes in the N-terminal cap.
  Phys Chem Chem Phys, 11, 5437-5444.  
19636808 D.M.Tiede, K.L.Mardis, and X.Zuo (2009).
X-ray scattering combined with coordinate-based analyses for applications in natural and artificial photosynthesis.
  Photosynth Res, 102, 267-279.  
19091750 J.Hendriks, and K.J.Hellingwerf (2009).
pH Dependence of the Photoactive Yellow Protein Photocycle Recovery Reaction Reveals a New Late Photocycle Intermediate with a Deprotonated Chromophore.
  J Biol Chem, 284, 5277-5288.  
18922794 K.Emami, E.Topakas, T.Nagy, J.Henshaw, K.A.Jackson, K.E.Nelson, E.F.Mongodin, J.W.Murray, R.J.Lewis, and H.J.Gilbert (2009).
Regulation of the Xylan-degrading Apparatus of Cellvibrio japonicus by a Novel Two-component System.
  J Biol Chem, 284, 1086-1096.
PDB code: 2va0
19707683 K.Okamoto, N.Hamada, T.A.Okamura, N.Ueyama, and H.Yamamoto (2009).
Color regulation and stabilization of chromophore by Cys69 in photoactive yellow protein active center.
  Org Biomol Chem, 7, 3782-3791.  
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
19470452 P.A.Sigala, M.A.Tsuchida, and D.Herschlag (2009).
Hydrogen bond dynamics in the active site of photoactive yellow protein.
  Proc Natl Acad Sci U S A, 106, 9232-9237.  
19122140 S.Yamaguchi, H.Kamikubo, K.Kurihara, R.Kuroki, N.Niimura, N.Shimizu, Y.Yamazaki, and M.Kataoka (2009).
Low-barrier hydrogen bond in photoactive yellow protein.
  Proc Natl Acad Sci U S A, 106, 440-444.
PDB codes: 2zoh 2zoi
18794212 B.C.Lee, and W.D.Hoff (2008).
Proline 54 trans-cis isomerization is responsible for the kinetic partitioning at the last-step photocycle of photoactive yellow protein.
  Protein Sci, 17, 2101-2110.  
18214984 J.Vreede, K.J.Hellingwerf, and P.G.Bolhuis (2008).
Helix formation is a dynamical bottleneck in the recovery reaction of Photoactive Yellow Protein.
  Proteins, 72, 136-149.  
18513230 M.Harigai, M.Kataoka, and Y.Imamoto (2008).
Interaction between N-terminal loop and beta-scaffold of photoactive yellow protein.
  Photochem Photobiol, 84, 1031-1037.  
18399917 M.Kumauchi, M.T.Hara, P.Stalcup, A.Xie, and W.D.Hoff (2008).
Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor.
  Photochem Photobiol, 84, 956-969.  
18547519 P.D.Coureux, Z.P.Fan, V.Stojanoff, and U.K.Genick (2008).
Picometer-scale conformational heterogeneity separates functional from nonfunctional states of a photoreceptor protein.
  Structure, 16, 863-872.
PDB codes: 2qj5 2qj7
18399923 R.Nakamura, N.Hamada, H.Ichida, F.Tokunaga, and Y.Kanematsu (2008).
Transient vibronic structure in ultrafast fluorescence spectra of photoactive yellow protein.
  Photochem Photobiol, 84, 937-940.  
18480905 T.Matsuhira, H.Yamamoto, T.A.Okamura, and N.Ueyama (2008).
Manipulation of an intramolecular NH...O hydrogen bond by photoswitching between stable E/Z isomers of the cinnamate framework.
  Org Biomol Chem, 6, 1926-1933.  
18698471 T.Matsuhira, K.Tsuchihashi, H.Yamamoto, T.A.Okamura, and N.Ueyama (2008).
Novel photosystem involving protonation and deprotonation processes modelled on a PYP photocycle.
  Org Biomol Chem, 6, 3118-3126.  
18399916 Y.Imamoto, M.Harigai, T.Morimoto, and M.Kataoka (2008).
Low-temperature spectroscopy of Met100Ala mutant of photoactive yellow protein.
  Photochem Photobiol, 84, 970-976.  
18227128 Y.Imamoto, S.Tatsumi, M.Harigai, Y.Yamazaki, H.Kamikubo, and M.Kataoka (2008).
Diverse roles of glycine residues conserved in photoactive yellow proteins.
  Biophys J, 94, 3620-3628.  
17223691 A.Pandini, M.S.Denison, Y.Song, A.A.Soshilov, and L.Bonati (2007).
Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis.
  Biochemistry, 46, 696-708.  
17496031 D.Hoersch, H.Otto, C.P.Joshi, B.Borucki, M.A.Cusanovich, and M.P.Heyn (2007).
Role of a conserved salt bridge between the PAS core and the N-terminal domain in the activation of the photoreceptor photoactive yellow protein.
  Biophys J, 93, 1687-1699.  
17307829 H.Kamikubo, N.Shimizu, M.Harigai, Y.Yamazaki, Y.Imamoto, and M.Kataoka (2007).
Characterization of the solution structure of the M intermediate of photoactive yellow protein using high-angle solution x-ray scattering.
  Biophys J, 92, 3633-3642.  
17416661 J.Krämer, J.D.Fischer, E.Zientz, V.Vijayan, C.Griesinger, A.Lupas, and G.Unden (2007).
Citrate sensing by the C4-dicarboxylate/citrate sensor kinase DcuS of Escherichia coli: binding site and conversion of DcuS to a C4-dicarboxylate- or citrate-specific sensor.
  J Bacteriol, 189, 4290-4298.  
17373703 K.Shirai, Y.Yamazaki, H.Kamikubo, Y.Imamoto, and M.Kataoka (2007).
Attempt to simplify the amino-acid sequence of photoactive yellow protein with a set of simple rules.
  Proteins, 67, 821-833.  
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.  
18024131 M.A.van der Horst, J.Key, and K.J.Hellingwerf (2007).
Photosensing in chemotrophic, non-phototrophic bacteria: let there be light sensing too.
  Trends Microbiol, 15, 554-562.  
18093935 R.A.Nome, J.M.Zhao, W.D.Hoff, and N.F.Scherer (2007).
Axis-dependent anisotropy in protein unfolding from integrated nonequilibrium single-molecule experiments, analysis, and simulation.
  Proc Natl Acad Sci U S A, 104, 20799-20804.  
18067379 R.Nakamura, N.Hamada, H.Ichida, F.Tokunaga, and Y.Kanematsu (2007).
Coherent oscillations in ultrafast fluorescence of photoactive yellow protein.
  J Chem Phys, 127, 215102.  
18007033 S.Z.Fisher, S.Anderson, R.Henning, K.Moffat, P.Langan, P.Thiyagarajan, and A.J.Schultz (2007).
Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP).
  Acta Crystallogr D Biol Crystallogr, 63, 1178-1184.
PDB code: 2qws
16520375 A.Chapman-Smith, and M.L.Whitelaw (2006).
Novel DNA binding by a basic helix-loop-helix protein. The role of the dioxin receptor PAS domain.
  J Biol Chem, 281, 12535-12545.  
16829563 B.Borucki, C.P.Joshi, H.Otto, M.A.Cusanovich, and M.P.Heyn (2006).
The transient accumulation of the signaling state of photoactive yellow protein is controlled by the external pH.
  Biophys J, 91, 2991-3001.  
16761084 B.Borucki (2006).
Proton transfer in the photoreceptors phytochrome and photoactive yellow protein.
  Photochem Photobiol Sci, 5, 553-566.  
16634087 H.Zheng, J.Zhao, W.Sheng, and X.Q.Xie (2006).
A transmembrane helix-bundle from G-protein coupled receptor CB2: biosynthesis, purification, and NMR characterization.
  Biopolymers, 83, 46-61.  
16407155 I.R.Lee, W.Lee, and A.H.Zewail (2006).
Primary steps of the photoactive yellow protein: isolated chromophore dynamics and protein directed function.
  Proc Natl Acad Sci U S A, 103, 258-262.  
16855050 J.M.Zhao, H.Lee, R.A.Nome, S.Majid, N.F.Scherer, and W.D.Hoff (2006).
Single-molecule detection of structural changes during Per-Arnt-Sim (PAS) domain activation.
  Proc Natl Acad Sci U S A, 103, 11561-11566.  
16513745 K.J.Watts, K.Sommer, S.L.Fry, M.S.Johnson, and B.L.Taylor (2006).
Function of the N-terminal cap of the PAS domain in signaling by the aerotaxis receptor Aer.
  J Bacteriol, 188, 2154-2162.  
17015839 L.J.van Wilderen, M.A.van der Horst, I.H.van Stokkum, K.J.Hellingwerf, R.van Grondelle, and M.L.Groot (2006).
Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein.
  Proc Natl Acad Sci U S A, 103, 15050-15055.  
17144696 Groot, W.J.Buma, E.V.Gromov, I.Burghardt, H.Köppel, and L.S.Cederbaum (2006).
Combined experimental-theoretical study of the lower excited singlet states of paravinyl phenol, an analog of the paracoumaric acid chromophore.
  J Chem Phys, 125, 204303.  
16952373 R.Brudler, C.R.Gessner, S.Li, S.Tyndall, E.D.Getzoff, and V.L.Woods (2006).
PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry.
  J Mol Biol, 363, 148-160.  
16462939 S.B.Nabuurs, C.A.Spronk, G.W.Vuister, and G.Vriend (2006).
Traditional biomolecular structure determination by NMR spectroscopy allows for major errors.
  PLoS Comput Biol, 2, e9.  
17158704 T.Mascher, J.D.Helmann, and G.Unden (2006).
Stimulus perception in bacterial signal-transducing histidine kinases.
  Microbiol Mol Biol Rev, 70, 910-938.  
16557322 T.Matsuhira, H.Yamamoto, A.Onoda, T.A.Okamura, and N.Ueyama (2006).
Photoinduced switching of intramolecular hydrogen bond between amide NH and carboxyl oxygen.
  Org Biomol Chem, 4, 1338-1342.  
15653739 B.Nie, J.Stutzman, and A.Xie (2005).
A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues.
  Biophys J, 88, 2833-2847.  
15884065 D.S.Larsen, and R.van Grondelle (2005).
Initial photoinduced dynamics of the photoactive yellow protein.
  Chemphyschem, 6, 828-837.  
15870207 H.Ihee, S.Rajagopal, V.Srajer, R.Pahl, S.Anderson, M.Schmidt, F.Schotte, P.A.Anfinrud, M.Wulff, and K.Moffat (2005).
Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.
  Proc Natl Acad Sci U S A, 102, 7145-7150.
PDB codes: 1ts0 1ts6 1ts7 1ts8
15781452 H.Kneuper, I.G.Janausch, V.Vijayan, M.Zweckstetter, V.Bock, C.Griesinger, and G.Unden (2005).
The nature of the stimulus and of the fumarate binding site of the fumarate sensor DcuS of Escherichia coli.
  J Biol Chem, 280, 20596-20603.  
15813893 H.Zheng, J.Zhao, S.Wang, C.M.Lin, T.Chen, D.H.Jones, C.Ma, S.Opella, and X.Q.Xie (2005).
Biosynthesis and purification of a hydrophobic peptide from transmembrane domains of G-protein-coupled CB2 receptor.
  J Pept Res, 65, 450-458.  
16040745 I.B.Nielsen, S.Boyé-Péronne, M.O.El Ghazaly, M.B.Kristensen, S.Brøndsted Nielsen, and L.H.Andersen (2005).
Absorption spectra of photoactive yellow protein chromophores in vacuum.
  Biophys J, 89, 2597-2604.  
15722437 J.Vreede, W.Crielaard, K.J.Hellingwerf, and P.G.Bolhuis (2005).
Predicting the signaling state of photoactive yellow protein.
  Biophys J, 88, 3525-3535.  
15629718 O.Yildiz, M.Doi, I.Yujnovsky, L.Cardone, A.Berndt, S.Hennig, S.Schulze, C.Urbanke, P.Sassone-Corsi, and E.Wolf (2005).
Crystal structure and interactions of the PAS repeat region of the Drosophila clock protein PERIOD.
  Mol Cell, 17, 69-82.
PDB code: 1wa9
15146503 A.Yamada, T.Ishikura, and T.Yamato (2004).
Role of protein in the primary step of the photoreaction of yellow protein.
  Proteins, 55, 1063-1069.  
15146504 A.Yamada, T.Ishikura, and T.Yamato (2004).
Direct measure of functional importance visualized atom-by-atom for photoactive yellow protein: application to photoisomerization reaction.
  Proteins, 55, 1070-1077.  
15041675 D.Pan, A.Philip, W.D.Hoff, and R.A.Mathies (2004).
Time-resolved resonance raman structural studies of the pB' intermediate in the photocycle of photoactive yellow protein.
  Biophys J, 86, 2374-2382.  
14982921 H.Kurokawa, D.S.Lee, M.Watanabe, I.Sagami, B.Mikami, C.S.Raman, and T.Shimizu (2004).
A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor.
  J Biol Chem, 279, 20186-20193.
PDB codes: 1v9y 1v9z
15009198 M.H.Hefti, K.J.Françoijs, 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.  
15041745 M.Schmidt, R.Pahl, V.Srajer, S.Anderson, Z.Ren, H.Ihee, S.Rajagopal, and K.Moffat (2004).
Protein kinetics: structures of intermediates and reaction mechanism from time-resolved x-ray data.
  Proc Natl Acad Sci U S A, 101, 4799-4804.
PDB codes: 1s4r 1s4s
15583378 M.Sugishima, N.Tanimoto, K.Soda, N.Hamada, F.Tokunaga, and K.Fukuyama (2004).
Structure of photoactive yellow protein (PYP) E46Q mutant at 1.2 A resolution suggests how Glu46 controls the spectroscopic and kinetic characteristics of PYP.
  Acta Crystallogr D Biol Crystallogr, 60, 2305-2309.
PDB code: 1ugu
15096497 M.Unno, M.Kumauchi, N.Hamada, F.Tokunaga, and S.Yamauchi (2004).
Resonance Raman evidence for two conformations involved in the L intermediate of photoactive yellow protein.
  J Biol Chem, 279, 23855-23858.  
15326296 P.Pellicena, D.S.Karow, E.M.Boon, M.A.Marletta, and J.Kuriyan (2004).
Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases.
  Proc Natl Acad Sci U S A, 101, 12854-12859.
PDB codes: 1u4h 1u55 1u56
14643885 R.J.Kewley, M.L.Whitelaw, and A.Chapman-Smith (2004).
The mammalian basic helix-loop-helix/PAS family of transcriptional regulators.
  Int J Biochem Cell Biol, 36, 189-204.  
15026418 R.Kort, K.J.Hellingwerf, and R.B.Ravelli (2004).
Initial events in the photocycle of photoactive yellow protein.
  J Biol Chem, 279, 26417-26424.
PDB codes: 1uwn 1uwp
15159559 S.Anderson, S.Crosson, and K.Moffat (2004).
Short hydrogen bonds in photoactive yellow protein.
  Acta Crystallogr D Biol Crystallogr, 60, 1008-1016.
PDB codes: 1ot6 1ot9 1ota 1otb 1otd 1ote 1oti
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
15466030 S.Herrmann, Q.Ma, M.S.Johnson, A.V.Repik, and B.L.Taylor (2004).
PAS domain of the Aer redox sensor requires C-terminal residues for native-fold formation and flavin adenine dinucleotide binding.
  J Bacteriol, 186, 6782-6791.  
12496261 A.Haker, J.Hendriks, I.H.van Stokkum, J.Heberle, K.J.Hellingwerf, W.Crielaard, and T.Gensch (2003).
The two photocycles of photoactive yellow protein from Rhodobacter sphaeroides.
  J Biol Chem, 278, 8442-8451.  
12873139 B.Borucki, H.Otto, C.P.Joshi, C.Gasperi, M.A.Cusanovich, S.Devanathan, G.Tollin, and M.P.Heyn (2003).
pH Dependence of the photocycle kinetics of the E46Q mutant of photoactive yellow protein: protonation equilibrium between I1 and I2 intermediates, chromophore deprotonation by hydroxyl uptake, and protonation relaxation of the dark state.
  Biochemistry, 42, 8780-8790.  
12590594 E.Chen, T.Gensch, A.B.Gross, J.Hendriks, K.J.Hellingwerf, and D.S.Kliger (2003).
Dynamics of protein and chromophore structural changes in the photocycle of photoactive yellow protein monitored by time-resolved optical rotatory dispersion.
  Biochemistry, 42, 2062-2071.  
12872160 E.D.Getzoff, K.N.Gutwin, and U.K.Genick (2003).
Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation.
  Nat Struct Biol, 10, 663-668.
PDB code: 1nwz
12907723 G.Natrajan, M.H.Lamers, J.H.Enzlin, H.H.Winterwerp, A.Perrakis, and T.K.Sixma (2003).
Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates.
  Nucleic Acids Res, 31, 4814-4821.
PDB codes: 1oh5 1oh6 1oh7 1oh8
12589064 H.Hasegawa, S.Zinsser, Y.Rhee, E.O.Vik-Mo, S.Davanger, and J.C.Hay (2003).
Mammalian ykt6 is a neuronal SNARE targeted to a specialized compartment by its profilin-like amino terminal domain.
  Mol Biol Cell, 14, 698-720.  
12549916 J.A.Kyndt, F.Vanrobaeys, J.C.Fitch, B.V.Devreese, T.E.Meyer, M.A.Cusanovich, and J.J.Van Beeumen (2003).
Heterologous production of Halorhodospira halophila holo-photoactive yellow protein through tandem expression of the postulated biosynthetic genes.
  Biochemistry, 42, 965-970.  
12547797 J.Hendriks, I.H.van Stokkum, and K.J.Hellingwerf (2003).
Deuterium isotope effects in the photocycle transitions of the photoactive yellow protein.
  Biophys J, 84, 1180-1191.  
12639952 J.Vreede, M.A.van der Horst, K.J.Hellingwerf, W.Crielaard, and D.M.van Aalten (2003).
PAS domains. Common structure and common flexibility.
  J Biol Chem, 278, 18434-18439.
PDB code: 1odv
12907689 L.Pappalardo, I.G.Janausch, V.Vijayan, E.Zientz, J.Junker, W.Peti, M.Zweckstetter, G.Unden, and C.Griesinger (2003).
The NMR structure of the sensory domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli.
  J Biol Chem, 278, 39185-39188.
PDB code: 1ojg
12718516 M.A.Cusanovich, and T.E.Meyer (2003).
Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism.
  Biochemistry, 42, 4759-4770.  
12609912 M.Schmidt, S.Rajagopal, Z.Ren, and K.Moffat (2003).
Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data.
  Biophys J, 84, 2112-2129.  
14668441 P.J.Erbel, P.B.Card, O.Karakuzu, R.K.Bruick, and K.H.Gardner (2003).
Structural basis for PAS domain heterodimerization in the basic helix--loop--helix-PAS transcription factor hypoxia-inducible factor.
  Proc Natl Acad Sci U S A, 100, 15504-15509.
PDB code: 1p97
12563032 S.Rajagopal, and K.Moffat (2003).
Crystal structure of a photoactive yellow protein from a sensor histidine kinase: conformational variability and signal transduction.
  Proc Natl Acad Sci U S A, 100, 1649-1654.
PDB code: 1mzu
12641464 T.E.Meyer, S.Devanathan, T.Woo, E.D.Getzoff, G.Tollin, and M.A.Cusanovich (2003).
Site-specific mutations provide new insights into the origin of pH effects and alternative spectral forms in the photoactive yellow protein from Halorhodospira halophila.
  Biochemistry, 42, 3319-3325.  
11964249 A.Losi, E.Polverini, B.Quest, and W.Gärtner (2002).
First evidence for phototropin-related blue-light receptors in prokaryotes.
  Biophys J, 82, 2627-2634.
PDB code: 1ium
12198141 A.Vannini, C.Volpari, C.Gargioli, E.Muraglia, R.Cortese, R.De Francesco, P.Neddermann, and S.D.Marco (2002).
The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA.
  EMBO J, 21, 4393-4401.
PDB code: 1h0m
12146967 B.Borucki, S.Devanathan, H.Otto, M.A.Cusanovich, G.Tollin, and M.P.Heyn (2002).
Kinetics of proton uptake and dye binding by photoactive yellow protein in wild type and in the E46Q and E46A mutants.
  Biochemistry, 41, 10026-10037.  
12167331 B.L.Montgomery, and J.C.Lagarias (2002).
Phytochrome ancestry: sensors of bilins and light.
  Trends Plant Sci, 7, 357-366.  
11714713 D.M.van Aalten, A.Haker, J.Hendriks, K.J.Hellingwerf, L.Joshua-Tor, and W.Crielaard (2002).
Engineering photocycle dynamics. Crystal structures and kinetics of three photoactive yellow protein hinge-bending mutants.
  J Biol Chem, 277, 6463-6468.
PDB codes: 1gsv 1gsw 1gsx
11914481 D.M.van Aalten, W.Crielaard, K.J.Hellingwerf, and L.Joshua-Tor (2002).
Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 A resolution.
  Acta Crystallogr D Biol Crystallogr, 58, 585-590.
PDB code: 1kou
11823471 E.A.Andreasen, R.L.Tanguay, R.E.Peterson, and W.Heideman (2002).
Identification of a critical amino acid in the aryl hydrocarbon receptor.
  J Biol Chem, 277, 13210-13218.  
12112690 G.Groenhof, M.F.Lensink, H.J.Berendsen, and A.E.Mark (2002).
Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes.
  Proteins, 48, 212-219.  
12112689 G.Groenhof, M.F.Lensink, H.J.Berendsen, J.G.Snijders, and A.E.Mark (2002).
Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore.
  Proteins, 48, 202-211.  
11867475 J.Hendriks, T.Gensch, L.Hviid, M.A.van Der Horst, K.J.Hellingwerf, and J.J.van Thor (2002).
Transient exposure of hydrophobic surface in the photoactive yellow protein monitored with Nile Red.
  Biophys J, 82, 1632-1643.  
11827538 J.Sasaki, M.Kumauchi, N.Hamada, T.Oka, and F.Tokunaga (2002).
Light-induced unfolding of photoactive yellow protein mutant M100L.
  Biochemistry, 41, 1915-1922.  
11937052 K.Edman, A.Royant, P.Nollert, C.A.Maxwell, E.Pebay-Peyroula, J.Navarro, R.Neutze, and E.M.Landau (2002).
Early structural rearrangements in the photocycle of an integral membrane sensory receptor.
  Structure, 10, 473-482.
PDB codes: 1gu8 1gue
11863442 K.Takeshita, Y.Imamoto, M.Kataoka, F.Tokunaga, and M.Terazima (2002).
Themodynamic and transport properties of intermediate states of the photocyclic reaction of photoactive yellow protein.
  Biochemistry, 41, 3037-3048.  
12202381 K.Takeshita, Y.Imamoto, M.Kataoka, K.Mihara, F.Tokunaga, and M.Terazima (2002).
Structural change of site-directed mutants of PYP: new dynamics during pR state.
  Biophys J, 83, 1567-1577.  
11969428 M.Unno, M.Kumauchi, J.Sasaki, F.Tokunaga, and S.Yamauchi (2002).
Resonance Raman spectroscopy and quantum chemical calculations reveal structural changes in the active site of photoactive yellow protein.
  Biochemistry, 41, 5668-5674.  
12511036 R.S.Liu (2002).
Introduction to the symposium-in-print: photoisomerization pathways, torsional relaxation and the hula twists.
  Photochem Photobiol, 76, 580-583.  
12427020 Y.Imamoto, H.Kamikubo, M.Harigai, N.Shimizu, and M.Kataoka (2002).
Light-induced global conformational change of photoactive yellow protein in solution.
  Biochemistry, 41, 13595-13601.  
11761333 B.L.Taylor, A.Rebbapragada, and M.S.Johnson (2001).
The FAD-PAS domain as a sensor for behavioral responses in Escherichia coli.
  Antioxid Redox Signal, 3, 867-879.  
11717509 M.Hefti, J.Hendle, C.Enroth, J.Vervoort, and P.A.Tucker (2001).
Crystallization and preliminary crystallographic data of the PAS domain of the NifL protein from Azotobacter vinelandii.
  Acta Crystallogr D Biol Crystallogr, 57, 1895-1896.  
11248020 S.Crosson, and K.Moffat (2001).
Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction.
  Proc Natl Acad Sci U S A, 98, 2995-3000.
PDB code: 1g28
11566800 S.Devanathan, S.Lin, M.A.Cusanovich, N.Woodbury, and G.Tollin (2001).
Early photocycle kinetic behavior of the E46A and Y42F mutants of photoactive yellow protein: femtosecond spectroscopy.
  Biophys J, 81, 2314-2319.  
11761327 W.R.Briggs, J.M.Christie, and M.Salomon (2001).
Phototropins: a new family of flavin-binding blue light receptors in plants.
  Antioxid Redox Signal, 3, 775-788.  
11724545 Y.Imamoto, K.Mihara, F.Tokunaga, and M.Kataoka (2001).
Spectroscopic characterization of the photocycle intermediates of photoactive yellow protein.
  Biochemistry, 40, 14336-14343.  
11705368 Z.Ren, B.Perman, V.Srajer, T.Y.Teng, C.Pradervand, D.Bourgeois, F.Schotte, T.Ursby, R.Kort, M.Wulff, and K.Moffat (2001).
A molecular movie at 1.8 A resolution displays the photocycle of photoactive yellow protein, a eubacterial blue-light receptor, from nanoseconds to seconds.
  Biochemistry, 40, 13788-13801.  
10844669 A.Repik, A.Rebbapragada, M.S.Johnson, J.O.Haznedar, I.B.Zhulin, and B.L.Taylor (2000).
PAS domain residues involved in signal transduction by the Aer redox sensor of Escherichia coli.
  Mol Microbiol, 36, 806-816.  
10944334 D.Bourgeois, U.Wagner, and M.Wulff (2000).
Towards automated Laue data processing: application to the choice of optimal X-ray spectrum.
  Acta Crystallogr D Biol Crystallogr, 56, 973-985.  
  10739248 D.M.van Aalten, W.Crielaard, K.J.Hellingwerf, and L.Joshua-Tor (2000).
Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility.
  Protein Sci, 9, 64-72.
PDB code: 1d7e
11058743 D.R.Flower, A.C.North, and C.E.Sansom (2000).
The lipocalin protein family: structural and sequence overview.
  Biochim Biophys Acta, 1482, 9.  
10653656 E.Demchuk, U.K.Genick, T.T.Woo, E.D.Getzoff, and D.Bashford (2000).
Protonation states and pH titration in the photocycle of photoactive yellow protein.
  Biochemistry, 39, 1100-1113.  
10713511 G.J.Kleywegt (2000).
Validation of protein crystal structures.
  Acta Crystallogr D Biol Crystallogr, 56, 249-265.  
10891070 H.Kandori, T.Iwata, J.Hendriks, A.Maeda, and K.J.Hellingwerf (2000).
Water structural changes involved in the activation process of photoactive yellow protein.
  Biochemistry, 39, 7902-7909.  
11063584 R.Brudler, T.E.Meyer, U.K.Genick, S.Devanathan, T.T.Woo, D.P.Millar, K.Gerwert, M.A.Cusanovich, G.Tollin, and E.D.Getzoff (2000).
Coupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein.
  Biochemistry, 39, 13478-13486.
PDB codes: 1f98 1f9i
11023916 S.Devanathan, S.Lin, M.A.Cusanovich, N.Woodbury, and G.Tollin (2000).
Early intermediates in the photocycle of the Glu46Gln mutant of photoactive yellow protein: femtosecond spectroscopy.
  Biophys J, 79, 2132-2137.  
10712916 S.H.Soderling, and J.A.Beavo (2000).
Regulation of cAMP and cGMP signaling: new phosphodiesterases and new functions.
  Curr Opin Cell Biol, 12, 174-179.  
10811894 S.I.Bibikov, L.A.Barnes, Y.Gitin, and J.S.Parkinson (2000).
Domain organization and flavin adenine dinucleotide-binding determinants in the aerotaxis signal transducer Aer of Escherichia coli.
  Proc Natl Acad Sci U S A, 97, 5830-5835.  
  10739264 T.M.Weaver (2000).
The pi-helix translates structure into function.
  Protein Sci, 9, 201-206.  
11032796 Y.S.Ho, L.M.Burden, and J.H.Hurley (2000).
Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor.
  EMBO J, 19, 5288-5299.
PDB codes: 1f5m 1fl4
  10357859 B.L.Taylor, and I.B.Zhulin (1999).
PAS domains: internal sensors of oxygen, redox potential, and light.
  Microbiol Mol Biol Rev, 63, 479-506.  
10364204 J.Hendriks, W.D.Hoff, W.Crielaard, and K.J.Hellingwerf (1999).
Protonation/deprotonation reactions triggered by photoactivation of photoactive yellow protein from Ectothiorhodospira halophila.
  J Biol Chem, 274, 17655-17660.  
10508688 S.T.Crews, and C.M.Fan (1999).
Remembrance of things PAS: regulation of development by bHLH-PAS proteins.
  Curr Opin Genet Dev, 9, 580-587.  
9893997 W.D.Hoff, A.Xie, I.H.Van Stokkum, X.J.Tang, J.Gural, A.R.Kroon, and K.J.Hellingwerf (1999).
Global conformational changes upon receptor stimulation in photoactive yellow protein.
  Biochemistry, 38, 1009-1017.  
9818266 B.L.Stoddard (1998).
New results using Laue diffraction and time-resolved crystallography.
  Curr Opin Struct Biol, 8, 612-618.  
9506946 B.Perman, V.Srajer, Z.Ren, T.Teng, C.Pradervand, T.Ursby, D.Bourgeois, F.Schotte, M.Wulff, R.Kort, K.Hellingwerf, and K.Moffat (1998).
Energy transduction on the nanosecond time scale: early structural events in a xanthopsin photocycle.
  Science, 279, 1946-1950.
PDB code: 2pyr
9628473 G.K.Farber (1998).
Sensing photons.
  Nat Struct Biol, 5, 415-417.  
9665170 G.Rubinstenn, G.W.Vuister, F.A.Mulder, P.E.Düx, R.Boelens, K.J.Hellingwerf, and R.Kaptein (1998).
Structural and dynamic changes of photoactive yellow protein during its photocycle in solution.
  Nat Struct Biol, 5, 568-570.  
9600888 J.L.Pellequer, K.A.Wager-Smith, S.A.Kay, and E.D.Getzoff (1998).
Photoactive yellow protein: a structural prototype for the three-dimensional fold of the PAS domain superfamily.
  Proc Natl Acad Sci U S A, 95, 5884-5890.
PDB code: 2arn
9649398 L.Ujj, S.Devanathan, T.E.Meyer, M.A.Cusanovich, G.Tollin, and G.H.Atkinson (1998).
New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: picosecond transient absorption spectroscopy.
  Biophys J, 75, 406-412.  
9737845 P.Düx, G.Rubinstenn, G.W.Vuister, R.Boelens, F.A.Mulder, K.Hård, W.D.Hoff, A.R.Kroon, W.Crielaard, K.J.Hellingwerf, and R.Kaptein (1998).
Solution structure and backbone dynamics of the photoactive yellow protein.
  Biochemistry, 37, 12689-12699.
PDB code: 3phy
9636160 R.Cordfunke, R.Kort, A.Pierik, B.Gobets, G.J.Koomen, J.W.Verhoeven, and K.J.Hellingwerf (1998).
Trans/cis (Z/E) photoisomerization of the chromophore of photoactive yellow protein is not a prerequisite for the initiation of the photocycle of this photoreceptor protein.
  Proc Natl Acad Sci U S A, 95, 7396-7401.  
9708992 S.Devanathan, U.K.Genick, I.L.Canestrelli, T.E.Meyer, M.A.Cusanovich, E.D.Getzoff, and G.Tollin (1998).
New insights into the photocycle of Ectothiorhodospira halophila photoactive yellow protein: photorecovery of the long-lived photobleached intermediate in the Met100Ala mutant.
  Biochemistry, 37, 11563-11568.  
9715903 T.Yamato, N.Niimura, and N.Go (1998).
Molecular dynamics study of femtosecond events in photoactive yellow protein after photoexcitation of the chromophore.
  Proteins, 32, 268-275.  
9382818 C.P.Ponting, and L.Aravind (1997).
PAS: a multifunctional domain family comes to light.
  Curr Biol, 7, R674-R677.  
9197235 G.K.Farber (1997).
Laue crystallography: Lights! Camera! action!
  Curr Biol, 7, R352-R354.  
9261074 I.Schlichting, and J.Berendzen (1997).
Out of the blue: the photocycle of the photoactive yellow protein.
  Structure, 5, 735-739.  
9402704 P.Ballario, and G.Macino (1997).
White collar proteins: PASsing the light signal in Neurospora crassa.
  Trends Microbiol, 5, 458-462.  
8993312 U.K.Genick, S.Devanathan, T.E.Meyer, I.L.Canestrelli, E.Williams, M.A.Cusanovich, G.Tollin, and E.D.Getzoff (1997).
Active site mutants implicate key residues for control of color and light cycle kinetics of photoactive yellow protein.
  Biochemistry, 36, 8.  
9148894 Y.Imamoto, K.Mihara, O.Hisatomi, M.Kataoka, F.Tokunaga, N.Bojkova, and K.Yoshihara (1997).
Evidence for proton transfer from Glu-46 to the chromophore during the photocycle of photoactive yellow protein.
  J Biol Chem, 272, 12905-12908.  
8943241 A.R.Kroon, W.D.Hoff, H.P.Fennema, J.Gijzen, G.J.Koomen, J.W.Verhoeven, W.Crielaard, and K.J.Hellingwerf (1996).
Spectral tuning, fluorescence, and photoactivity in hybrids of photoactive yellow protein, reconstituted with native or modified chromophores.
  J Biol Chem, 271, 31949-31956.  
8942626 A.Xie, W.D.Hoff, A.R.Kroon, and K.J.Hellingwerf (1996).
Glu46 donates a proton to the 4-hydroxycinnamate anion chromophore during the photocycle of photoactive yellow protein.
  Biochemistry, 35, 14671-14678.  
8804619 M.E.Van Brederode, W.D.Hoff, I.H.Van Stokkum, M.L.Groot, and K.J.Hellingwerf (1996).
Protein folding thermodynamics applied to the photocycle of the photoactive yellow protein.
  Biophys J, 71, 365-380.  
8611556 M.Koh, G.Van Driessche, B.Samyn, W.D.Hoff, T.E.Meyer, M.A.Cusanovich, and J.J.Van Beeumen (1996).
Sequence evidence for strong conservation of the photoactive yellow proteins from the halophilic phototrophic bacteria Chromatium salexigens and Rhodospirillum salexigens.
  Biochemistry, 35, 2526-2534.  
  8670821 R.Kort, W.D.Hoff, M.Van West, A.R.Kroon, S.M.Hoffer, K.H.Vlieg, W.Crielaand, J.J.Van Beeumen, and K.J.Hellingwerf (1996).
The xanthopsins: a new family of eubacterial blue-light photoreceptors.
  EMBO J, 15, 3209-3218.  
8573584 W.D.Hoff, B.Devreese, R.Fokkens, I.M.Nugteren-Roodzant, J.Van Beeumen, N.Nibbering, and K.J.Hellingwerf (1996).
Chemical reactivity and spectroscopy of the thiol ester-linked p-coumaric acid chromophore in the photoactive yellow protein from Ectothiorhodospira halophila.
  Biochemistry, 35, 1274-1281.  
8916889 Y.Imamoto, M.Kataoka, and F.Tokunaga (1996).
Photoreaction cycle of photoactive yellow protein from Ectothiorhodospira halophila studied by low-temperature spectroscopy.
  Biochemistry, 35, 14047-14053.  
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