PDBsum entry 2pyp

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Photoreceptor PDB id
Protein chain
125 a.a. *
Waters ×56
* Residue conservation analysis
PDB id:
Name: Photoreceptor
Title: Photoactive yellow protein, photostationary state, 50% ground state, 50% bleached
Structure: Photoactive yellow protein. Chain: a
Source: Halorhodospira halophila. Organism_taxid: 1053. Strain: bn9626
1.90Å     R-factor:   0.204    
Authors: U.K.Genick,G.E.O.Borgstahl,K.Ng,Z.Ren,C.Pradervand,P.Burke, V.Srajer,T.Teng,W.Schildkamp,D.E.Mcree,K.Moffat,E.D.Getzoff
Key ref:
U.K.Genick et al. (1997). Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Science, 275, 1471-1475. PubMed id: 9045611 DOI: 10.1126/science.275.5305.1471
03-Feb-97     Release date:   29-Apr-98    
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: 10.1126/science.275.5305.1471 Science 275:1471-1475 (1997)
PubMed id: 9045611  
Structure of a protein photocycle intermediate by millisecond time-resolved crystallography.
U.K.Genick, G.E.Borgstahl, K.Ng, Z.Ren, C.Pradervand, P.M.Burke, V.Srajer, T.Y.Teng, W.Schildkamp, D.E.McRee, K.Moffat, E.D.Getzoff.
The blue-light photoreceptor photoactive yellow protein (PYP) undergoes a self-contained light cycle. The atomic structure of the bleached signaling intermediate in the light cycle of PYP was determined by millisecond time-resolved, multiwavelength Laue crystallography and simultaneous optical spectroscopy. Light-induced trans-to-cis isomerization of the 4-hydroxycinnamyl chromophore and coupled protein rearrangements produce a new set of active-site hydrogen bonds. An arginine gateway opens, allowing solvent exposure and protonation of the chromophore's phenolic oxygen. Resulting changes in shape, hydrogen bonding, and electrostatic potential at the protein surface form a likely basis for signal transduction. The structural results suggest a general framework for the interpretation of protein photocycles.
  Selected figure(s)  
Figure 1.
Fig. 1. Chromophore structure (left) and difference (|F[photostationary]| |F[dark]|) electron density map with PYP fold in the^ ground state (white ribbon) and trans-chromophore (yellow) (right). The density map (contoured at 3 ) shows an excellent signal-to-noise^ ratio for the transient, light-induced, structural changes. The^ largest signal is localized at the active site (blue, positive; and red, negative electron density). Figures 1 to 4 were made^ with AVS (28).
Figure 4.
Fig. 4. Solvent-accessible molecular surface of PYP in (A) the dark state and (C) bleached state color-coded for electrostatic^ potential as calculated by DelPhi (29) (deep red, < 4 kT; white, neutral; dark blue, >4 kT). Partial charges were assigned according to a revised version of the CHARMM force field (30). In (B), C[ ]traces and side chains of Arg52 for the dark (yellow) and bleached (white) states are shown. Bleaching increases the positive electrostatic potential at the^ active site. Movements of Arg52 and the chromophore change the surface shape.
  The above figures are reprinted by permission from the AAAs: Science (1997, 275, 1471-1475) copyright 1997.  
  Figures were selected by an automated process.  

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.
  J Synchrotron Radiat, 19, 264-273.  
20431017 A.B.Wöhri, G.Katona, L.C.Johansson, E.Fritz, E.Malmerberg, M.Andersson, J.Vincent, M.Eklund, M.Cammarata, M.Wulff, J.Davidsson, G.Groenhof, and R.Neutze (2010).
Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction.
  Science, 328, 630-633.
PDB codes: 2x5u 2x5v
20133629 G.Hummer (2010).
Catching a protein in the act.
  Proc Natl Acad Sci U S A, 107, 2381-2382.  
20856983 P.Changenet-Barret, C.Loukou, C.Ley, F.Lacombat, P.Plaza, J.M.Mallet, and M.M.Martin (2010).
Primary photodynamics of a biomimetic model of photoactive yellow protein (PYP).
  Phys Chem Chem Phys, 12, 13715-13723.  
20164644 S.Westenhoff, E.Nazarenko, E.Malmerberg, J.Davidsson, G.Katona, and R.Neutze (2010).
Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches.
  Acta Crystallogr A, 66, 207-219.  
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.  
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.  
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.  
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.  
18348979 J.Cheung, C.A.Bingman, M.Reyngold, W.A.Hendrickson, and C.D.Waldburger (2008).
Crystal structure of a functional dimer of the PhoQ sensor domain.
  J Biol Chem, 283, 13762-13770.
PDB codes: 3bq8 3bqa
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.  
18096633 M.Laberge, and T.Yonetani (2008).
Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: effector-linked perturbation of tertiary conformations and HbA concerted dynamics.
  Biophys J, 94, 2737-2751.  
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
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.  
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.  
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
17881820 U.K.Genick (2007).
Structure-factor extrapolation using the scalar approximation: theory, applications and limitations.
  Acta Crystallogr D Biol Crystallogr, 63, 1029-1041.  
16847839 A.Espagne, D.H.Paik, P.Changenet-Barret, M.M.Martin, and A.H.Zewail (2006).
Ultrafast photoisomerization of photoactive yellow protein chromophore analogues in solution: influence of the protonation state.
  Chemphyschem, 7, 1717-1726.  
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.  
16709144 H.Yamada, M.Kumauchi, N.Hamada, X.G.Zheng, I.H.Park, K.Masuda, K.Yoshihara, and F.Tokunaga (2006).
Analogue chromophore study of the influence of electronic perturbation on color regulation of photoactive yellow protein.
  Photochem Photobiol, 82, 1422-1425.  
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.  
16500975 J.S.Khan, Y.Imamoto, M.Harigai, M.Kataoka, and M.Terazima (2006).
Conformational changes of PYP monitored by diffusion coefficient: effect of N-terminal alpha-helices.
  Biophys J, 90, 3686-3693.  
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.  
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.  
16513787 S.Yeremenko, I.H.van Stokkum, K.Moffat, and K.J.Hellingwerf (2006).
Influence of the crystalline state on photoinduced dynamics of photoactive yellow protein studied by ultraviolet-visible transient absorption spectroscopy.
  Biophys J, 90, 4224-4235.  
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
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.  
16258045 L.Premvardhan, M.A.van der Horst, K.J.Hellingwerf, and R.van Grondelle (2005).
How light-induced charge transfer accelerates the receptor-state recovery of photoactive yellow protein from its signaling state.
  Biophys J, 89, L64-L66.  
15642261 S.Rajagopal, S.Anderson, V.Srajer, M.Schmidt, R.Pahl, and K.Moffat (2005).
A structural pathway for signaling in the E46Q mutant of photoactive yellow protein.
  Structure, 13, 55-63.
PDB codes: 1t18 1t19 1t1a 1t1b 1t1c
15642256 S.Yeremenko, and K.J.Hellingwerf (2005).
Resolving protein structure dynamically.
  Structure, 13, 4-6.  
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.  
15345564 D.S.Larsen, I.H.van Stokkum, M.Vengris, M.A.van Der Horst, Weerd, K.J.Hellingwerf, and R.van Grondelle (2004).
Incoherent manipulation of the photoactive yellow protein photocycle with dispersed pump-dump-probe spectroscopy.
  Biophys J, 87, 1858-1872.  
15041690 D.S.Larsen, M.Vengris, I.H.van Stokkum, M.A.van der Horst, Weerd, K.J.Hellingwerf, and R.van Grondelle (2004).
Photoisomerization and photoionization of the photoactive yellow protein chromophore in solution.
  Biophys J, 86, 2538-2550.  
15477687 J.M.Cole (2004).
'In-situ' charge-density studies of photoinduced phenomena: possibilities for the future?
  Acta Crystallogr A, 60, 472-479.  
15466708 K.Itoh, and M.Sasai (2004).
Dynamical transition and proteinquake in photoactive yellow protein.
  Proc Natl Acad Sci U S A, 101, 14736-14741.  
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
15345563 M.Vengris, M.A.van der Horst, G.Zgrablic, I.H.van Stokkum, S.Haacke, M.Chergui, K.J.Hellingwerf, R.van Grondelle, and D.S.Larsen (2004).
Contrasting the excited-state dynamics of the photoactive yellow protein chromophore: protein versus solvent environments.
  Biophys J, 87, 1848-1857.  
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
15103131 S.Rajagopal, M.Schmidt, S.Anderson, H.Ihee, and K.Moffat (2004).
Analysis of experimental time-resolved crystallographic data by singular value decomposition.
  Acta Crystallogr D Biol Crystallogr, 60, 860-871.  
15063857 U.Jenal (2004).
Cyclic di-guanosine-monophosphate comes of age: a novel secondary messenger involved in modulating cell surface structures in bacteria?
  Curr Opin Microbiol, 7, 185-191.  
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
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.  
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.  
12939133 M.L.Groot, L.J.van Wilderen, D.S.Larsen, M.A.van der Horst, I.H.van Stokkum, K.J.Hellingwerf, and R.van Grondelle (2003).
Initial steps of signal generation in photoactive yellow protein revealed with femtosecond mid-infrared spectroscopy.
  Biochemistry, 42, 10054-10059.  
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.  
14661962 N.M.Derix, R.W.Wechselberger, M.A.van der Horst, K.J.Hellingwerf, R.Boelens, R.Kaptein, and N.A.van Nuland (2003).
Lack of negative charge in the E46Q mutant of photoactive yellow protein prevents partial unfolding of the blue-shifted intermediate.
  Biochemistry, 42, 14501-14506.  
12945580 R.Kort, R.B.Ravelli, F.Schotte, D.Bourgeois, W.Crielaard, K.J.Hellingwerf, and M.Wulff (2003).
Characterization of photocycle intermediates in crystalline photoactive yellow protein.
  Photochem Photobiol, 78, 131-137.  
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.  
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.  
12379689 C.Wagner, A.Saizieu Ad, H.J.Schönfeld, M.Kamber, R.Lange, C.J.Thompson, and M.G.Page (2002).
Genetic analysis and functional characterization of the Streptococcus pneumoniae vic operon.
  Infect Immun, 70, 6121-6128.  
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
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.  
11839490 H.J.Dyson, and P.E.Wright (2002).
Coupling of folding and binding for unstructured proteins.
  Curr Opin Struct Biol, 12, 54-60.  
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.  
12146966 Q.Xu, L.Baciou, P.Sebban, and M.R.Gunner (2002).
Exploring the energy landscape for Q(A)(-) to Q(B) electron transfer in bacterial photosynthetic reaction centers: effect of substrate position and tail length on the conformational gating step.
  Biochemistry, 41, 10021-10025.  
12211036 W.G.Krebs, V.Alexandrov, C.A.Wilson, N.Echols, H.Yu, and M.Gerstein (2002).
Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.
  Proteins, 48, 682-695.  
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.  
11297407 A.L.Chang, J.R.Tuckerman, G.Gonzalez, R.Mayer, H.Weinhouse, G.Volman, D.Amikam, M.Benziman, and M.A.Gilles-Gonzalez (2001).
Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor.
  Biochemistry, 40, 3420-3426.  
11783935 A.Royant, K.Edman, T.Ursby, E.Pebay-Peyroula, E.M.Landau, and R.Neutze (2001).
Spectroscopic characterization of bacteriorhodopsin's L-intermediate in 3D crystals cooled to 170 K.
  Photochem Photobiol, 74, 794-804.  
11470891 B.C.Lee, A.Pandit, P.A.Croonquist, and W.D.Hoff (2001).
Folding and signaling share the same pathway in a photoreceptor.
  Proc Natl Acad Sci U S A, 98, 9062-9067.  
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.  
11171992 H.Kandori, Y.Yamazaki, Y.Shichida, J.Raap, J.Lugtenburg, M.Belenky, and J.Herzfeld (2001).
Tight Asp-85--Thr-89 association during the pump switch of bacteriorhodopsin.
  Proc Natl Acad Sci U S A, 98, 1571-1576.  
16755302 J.E.Kim, D.W.McCamant, L.Zhu, and R.A.Mathies (2001).
Resonance Raman Structural Evidence that the Cis-to-Trans Isomerization in Rhodopsin Occurs in Femtoseconds.
  J Phys Chem B, 105, 1240-1249.  
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.  
11287643 V.Molina, and M.Merchán (2001).
On the absorbance changes in the photocycle of the photoactive yellow protein: a quantum-chemical analysis.
  Proc Natl Acad Sci U S A, 98, 4299-4304.  
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.  
11087391 C.J.Craven, N.M.Derix, J.Hendriks, R.Boelens, K.J.Hellingwerf, and R.Kaptein (2000).
Probing the nature of the blue-shifted intermediate of photoactive yellow protein in solution by NMR: hydrogen-deuterium exchange data and pH studies.
  Biochemistry, 39, 14392-14399.  
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
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.  
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.  
10625483 I.Rudik, A.Bell, P.J.Tonge, and C.Thorpe (2000).
4-Hydroxycinnamoyl-CoA: an ionizable probe of the active site of the medium chain acyl-CoA dehydrogenase.
  Biochemistry, 39, 92.  
11114513 I.Schlichting, and K.Chu (2000).
Trapping intermediates in the crystal: ligand binding to myoglobin.
  Curr Opin Struct Biol, 10, 744-752.  
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
10734184 W.G.Krebs, and M.Gerstein (2000).
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.
  Nucleic Acids Res, 28, 1665-1675.  
10836146 Y.Z.Gu, J.B.Hogenesch, and C.A.Bradfield (2000).
The PAS superfamily: sensors of environmental and developmental signals.
  Annu Rev Pharmacol Toxicol, 40, 519-561.  
9931023 A.T.Petkova, J.G.Hu, M.Bizounok, M.Simpson, R.G.Griffin, and J.Herzfeld (1999).
Arginine activity in the proton-motive photocycle of bacteriorhodopsin: solid-state NMR studies of the wild-type and D85N proteins.
  Biochemistry, 38, 1562-1572.  
  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.  
10359687 J.L.Pellequer, R.Brudler, and E.D.Getzoff (1999).
Biological sensors: More than one way to sense oxygen.
  Curr Biol, 9, R416-R418.  
10411952 J.M.Christie, M.Salomon, K.Nozue, M.Wada, and W.R.Briggs (1999).
LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): binding sites for the chromophore flavin mononucleotide.
  Proc Natl Acad Sci U S A, 96, 8779-8783.  
10226051 K.R.Rodgers (1999).
Heme-based sensors in biological systems.
  Curr Opin Chem Biol, 3, 158-167.  
10449801 N.Lebedev, and M.P.Timko (1999).
Protochlorophyllide oxidoreductase B-catalyzed protochlorophyllide photoreduction in vitro: insight into the mechanism of chlorophyll formation in light-adapted plants.
  Proc Natl Acad Sci U S A, 96, 9954-9959.  
10423446 S.Devanathan, A.Pacheco, L.Ujj, M.Cusanovich, G.Tollin, S.Lin, and N.Woodbury (1999).
Femtosecond spectroscopic observations of initial intermediates in the photocycle of the photoactive yellow protein from Ectothiorhodospira halophila.
  Biophys J, 77, 1017-1023.  
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.  
10611956 W.R.Briggs, and E.Huala (1999).
Blue-light photoreceptors in higher plants.
  Annu Rev Cell Dev Biol, 15, 33-62.  
10585916 W.Radding, T.Romo, and G.N.Phillips (1999).
Protein-assisted pericyclic reactions: an alternate hypothesis for the action of quantal receptors.
  Biophys J, 77, 2920-2929.  
10339561 W.Weber, V.Helms, J.A.McCammon, and P.W.Langhoff (1999).
Shedding light on the dark and weakly fluorescent states of green fluorescent proteins.
  Proc Natl Acad Sci U S A, 96, 6177-6182.  
9783749 B.L.Stoddard, B.E.Cohen, M.Brubaker, A.D.Mesecar, and D.E.Koshland (1998).
Millisecond Laue structures of an enzyme-product complex using photocaged substrate analogs.
  Nat Struct Biol, 5, 891-897.
PDB code: 1bl5
9818266 B.L.Stoddard (1998).
New results using Laue diffraction and time-resolved crystallography.
  Curr Opin Struct Biol, 8, 612-618.  
9759482 C.B.Hirschberg, P.W.Robbins, and C.Abeijon (1998).
Transporters of nucleotide sugars, ATP, and nucleotide sulfate in the endoplasmic reticulum and Golgi apparatus.
  Annu Rev Biochem, 67, 49-69.  
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
9699613 K.Moffat (1998).
Ultrafast time-resolved crystallography.
  Nat Struct Biol, 5, 641-643.  
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.  
9722650 M.Gerstein, and W.Krebs (1998).
A database of macromolecular motions.
  Nucleic Acids Res, 26, 4280-4290.  
9591684 N.Angelini, B.Corrias, A.Fissi, O.Pieroni, and F.Lenci (1998).
Photochromic polypeptides as synthetic models of biological photoreceptors: a spectroscopic study.
  Biophys J, 74, 2601-2610.  
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
10089512 R.B.Ravelli, M.L.Raves, Z.Ren, D.Bourgeois, M.Roth, J.Kroon, I.Silman, and J.L.Sussman (1998).
Static Laue diffraction studies on acetylcholinesterase.
  Acta Crystallogr D Biol Crystallogr, 54, 1359-1366.
PDB codes: 1ax9 2ack
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.  
9860942 W.Gong, B.Hao, S.S.Mansy, G.Gonzalez, M.A.Gilles-Gonzalez, and M.K.Chan (1998).
Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction.
  Proc Natl Acad Sci U S A, 95, 15177-15182.
PDB codes: 1bv5 1bv6 1drm 1drq
9761904 X.Yang, Z.Ren, and K.Moffat (1998).
Structure refinement against synchrotron Laue data: strategies for data collection and reduction.
  Acta Crystallogr D Biol Crystallogr, 54, 367-377.  
  9514261 Y.Cao, R.A.Musah, S.K.Wilcox, D.B.Goodin, and D.E.McRee (1998).
Protein conformer selection by ligand binding observed with crystallography.
  Protein Sci, 7, 72-78.
PDB code: 1ccj
9159101 A.Karlin (1997).
Transport bicycles.
  Proc Natl Acad Sci U S A, 94, 5508-5509.  
9315849 B.R.Crane, L.M.Siegel, and E.D.Getzoff (1997).
Probing the catalytic mechanism of sulfite reductase by X-ray crystallography: structures of the Escherichia coli hemoprotein in complex with substrates, inhibitors, intermediates, and products.
  Biochemistry, 36, 12120-12137.
PDB codes: 2gep 3geo 4gep 5gep 6gep 7gep 8gep
9414203 D.M.van Aalten, D.A.Conn, Groot, H.J.Berendsen, J.B.Findlay, and A.Amadei (1997).
Protein dynamics derived from clusters of crystal structures.
  Biophys J, 73, 2891-2896.  
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.  
9253408 J.E.Murphy, B.Stec, L.Ma, and E.R.Kantrowitz (1997).
Trapping and visualization of a covalent enzyme-phosphate intermediate.
  Nat Struct Biol, 4, 618-622.
PDB code: 1hjk
9667874 J.P.Wery, and R.W.Schevitz (1997).
New trends in macromolecular X-ray crystallography.
  Curr Opin Chem Biol, 1, 365-369.  
9345628 K.Moffat, and Z.Ren (1997).
Synchrotron radiation applications to macromolecular crystallography.
  Curr Opin Struct Biol, 7, 689-696.  
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