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PDBsum entry 3pyp

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Photoreceptor PDB id
3pyp
Jmol
Contents
Protein chain
125 a.a. *
Ligands
HC4
Waters ×138
* Residue conservation analysis
PDB id:
3pyp
Name: Photoreceptor
Title: Photoactive yellow protein, cryotrapped early light cycle intermediate
Structure: Photoactive yellow protein. Chain: a. Synonym: pyp. Other_details: thioester linkage between the sulfur of cys 69 and carboxy group of the 4-hydroxy cinnamic acid chromophore
Source: Halorhodospira halophila. Organism_taxid: 1053. Strain: bn9626
Resolution:
0.85Å     R-factor:   0.133     R-free:   0.155
Authors: U.K.Genick,S.M.Soltis,P.Kuhn,I.L.Canestrelli,E.D.Getzoff
Key ref:
U.K.Genick et al. (1998). Structure at 0.85 A resolution of an early protein photocycle intermediate. Nature, 392, 206-209. PubMed id: 9515969 DOI: 10.1038/32462
Date:
28-Jul-98     Release date:   01-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P16113  (PYP_HALHA) -  Photoactive yellow protein
Seq:
Struc:
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: 10.1038/32462 Nature 392:206-209 (1998)
PubMed id: 9515969  
 
 
Structure at 0.85 A resolution of an early protein photocycle intermediate.
U.K.Genick, S.M.Soltis, P.Kuhn, I.L.Canestrelli, E.D.Getzoff.
 
  ABSTRACT  
 
Protein photosensors from all kingdoms of life use bound organic molecules, known as chromophores, to detect light. A specific double bond within each chromophore is isomerized by light, triggering slower changes in the protein as a whole. The initial movements of the chromophore, which can occur in femtoseconds, are tightly constrained by the surrounding protein, making it difficult to see how isomerization can occur, be recognized, and be appropriately converted into a protein-wide structural change and biological signal. Here we report how this dilemma is resolved in the photoactive yellow protein (PYP). We trapped a key early intermediate in the light cycle of PYP at temperatures below -100 degrees C, and determined its structure at better than 1 A resolution. The 4-hydroxycinnamoyl chromophore isomerizes by flipping its thioester linkage with the protein, thus avoiding collisions resulting from large-scale movement of its aromatic ring during the initial light reaction. A protein-to-chromophore hydrogen bond that is present in both the preceding dark state and the subsequent signalling state of the photosensor breaks, forcing one of the hydrogen-bonding partners into a hydrophobic pocket. The isomerized bond is distorted into a conformation resembling that in the transition state. The resultant stored energy is used to drive the PYP light cycle. These results suggest a model for phototransduction, with implications for bacteriorhodopsin, photoactive proteins, PAS domains, and signalling proteins.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Structural consequences of light activation. a, Overview showing that electron-density differences (decrease in red basket weave, increase in blue basket weave) are restricted to the immediate vicinity of the chromophore (yellow stick figure). The overall fold is shown as a white ribbon. The F[light] - F[dark] difference map phased from the 1.4- ground-state model5 is contoured at 5 . b, Chemical drawings of the chromophore in the ground (dark; left) and light-activated (right) states. c, Stereo view of the active site showing refined models for the dark state (yellow) and the early intermediate (orange), with the difference electron density map described in a contoured at 4 . The difference map shows that chromophore isomerization took place by flipping the thioester linkage (lower centre) between the chromophore (Chr) and the protein. The difference map also shows minor adjustments in the surrounding protein.
Figure 3.
Figure 3 The environment of the thioester oxygen atom (O2) of the chromophore in the early intermediate. Instead of forming a hydrogen bond to the backbone amide of Cys 69 as in the preceding dark state (Fig. 2a) and subsequent signalling state (Fig. 2c), O2 is located in a hydrophobic pocket formed by three aromatic side chains (orange spheres) and the aromatic ring of the chromophore itself (orange sticks, top). We propose that the resolution of this mismatch and the re-formation of the O2-to-backbone hydrogen bond help to drive the formation of the bleached intermediate I2 (Fig. 2c) later in the photocycle.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 392, 206-209) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21220116 J.King-Scott, P.V.Konarev, S.Panjikar, R.Jordanova, D.I.Svergun, and P.A.Tucker (2011).
Structural characterization of the multidomain regulatory protein Rv1364c from Mycobacterium tuberculosis.
  Structure, 19, 56-69.  
21405157 K.Sneskov, T.Schwabe, J.Kongsted, and O.Christiansen (2011).
The polarizable embedding coupled cluster method.
  J Chem Phys, 134, 104108.  
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.  
20133629 G.Hummer (2010).
Catching a protein in the act.
  Proc Natl Acad Sci U S A, 107, 2381-2382.  
20141763 J.Rajput, D.B.Rahbek, G.Aravind, and L.H.Andersen (2010).
Spectral tuning of the photoactive yellow protein chromophore by H-bonding.
  Biophys J, 98, 488-492.  
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.  
20649309 Y.Wang, and H.Li (2010).
Excited state geometry of photoactive yellow protein chromophore: a combined conductorlike polarizable continuum model and time-dependent density functional study.
  J Chem Phys, 133, 034108.  
19475175 E.M.González, L.Guidoni, and C.Molteni (2009).
Chemical and protein shifts in the spectrum of the photoactive yellow protein: a time-dependent density functional theory/molecular mechanics study.
  Phys Chem Chem Phys, 11, 4556-4563.  
19655842 K.Kristensen, J.Kauczor, T.Kjaergaard, and P.Jørgensen (2009).
Quasienergy formulation of damped response theory.
  J Chem Phys, 131, 044112.  
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.  
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
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.  
18612842 E.Giraud, and A.Verméglio (2008).
Bacteriophytochromes in anoxygenic photosynthetic bacteria.
  Photosynth Res, 97, 141-153.  
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.  
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.  
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.  
17211076 J.E.McGeehan, P.Carpentier, A.Royant, D.Bourgeois, and R.B.Ravelli (2007).
X-ray radiation-induced damage in DNA monitored by online Raman.
  J Synchrotron Radiat, 14, 99.  
17470789 L.M.Frutos, T.Andruniów, F.Santoro, N.Ferré, and M.Olivucci (2007).
Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry.
  Proc Natl Acad Sci U S A, 104, 7764-7769.  
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.  
16761084 B.Borucki (2006).
Proton transfer in the photoreceptors phytochrome and photoactive yellow protein.
  Photochem Photobiol Sci, 5, 553-566.  
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.  
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 M.de 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.  
15884065 D.S.Larsen, and R.van Grondelle (2005).
Initial photoinduced dynamics of the photoactive yellow protein.
  Chemphyschem, 6, 828-837.  
16092146 D.Xie, and J.Zeng (2005).
Electronic excitations of green fluorescent proteins: protonation states of chromophore model compound in solutions.
  J Comput Chem, 26, 1487-1496.  
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.  
16366562 K.Heyne, O.F.Mohammed, A.Usman, J.Dreyer, E.T.Nibbering, and M.A.Cusanovich (2005).
Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein.
  J Am Chem Soc, 127, 18100-18106.  
16041073 R.Caliandro, B.Carrozzini, G.L.Cascarano, L.De Caro, C.Giacovazzo, and D.Siliqi (2005).
Ab initio phasing at resolution higher than experimental resolution.
  Acta Crystallogr D Biol Crystallogr, 61, 1080-1087.  
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
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.  
15345564 D.S.Larsen, I.H.van Stokkum, M.Vengris, M.A.van Der Horst, F.L.de 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, F.L.de 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.  
14975533 G.Alexandre, S.Greer-Phillips, and I.B.Zhulin (2004).
Ecological role of energy taxis in microorganisms.
  FEMS Microbiol Rev, 28, 113-126.  
14532280 K.Edman, A.Royant, G.Larsson, F.Jacobson, T.Taylor, D.van der Spoel, E.M.Landau, E.Pebay-Peyroula, and R.Neutze (2004).
Deformation of helix C in the low temperature L-intermediate of bacteriorhodopsin.
  J Biol Chem, 279, 2147-2158.
PDB codes: 1r3p 1vjm
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.  
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.  
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
15339224 S.Anderson, V.Srajer, and K.Moffat (2004).
Structural heterogeneity of cryotrapped intermediates in the bacterial blue light photoreceptor, photoactive yellow protein.
  Photochem Photobiol, 80, 7.  
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
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
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.  
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.  
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
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.  
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
12511039 M.Uda, T.Mizutani, J.Hayakawa, A.Momotake, M.Ikegami, R.Nagahata, and T.Arai (2002).
Photoisomerization of stilbene dendrimers: the need for a volume-conserving isomerization mechanisms.
  Photochem Photobiol, 76, 596-605.  
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.  
11914484 T.Ursby, M.Weik, E.Fioravanti, M.Delarue, M.Goeldner, and D.Bourgeois (2002).
Cryophotolysis of caged compounds: a technique for trapping intermediate states in protein crystals.
  Acta Crystallogr D Biol Crystallogr, 58, 607-614.
PDB codes: 1gsi 1gtv
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.  
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.  
11258940 Q.Xu, and M.R.Gunner (2001).
Trapping conformational intermediate states in the reaction center protein from photosynthetic bacteria.
  Biochemistry, 40, 3232-3241.  
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.  
10666594 D.Housset, F.Benabicha, V.Pichon-Pesme, C.Jelsch, A.Maierhofer, S.David, J.C.Fontecilla-Camps, and C.Lecomte (2000).
Towards the charge-density study of proteins: a room-temperature scorpion-toxin structure at 0.96 A resolution as a first test case.
  Acta Crystallogr D Biol Crystallogr, 56, 151-160.  
  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
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11114513 I.Schlichting, and K.Chu (2000).
Trapping intermediates in the crystal: ligand binding to myoglobin.
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Coupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein.
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PDB codes: 1f98 1f9i
11016972 R.S.Liu, and G.S.Hammond (2000).
The case of medium-dependent dual mechanisms for photoisomerization: one-bond-flip and hula-twist.
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Early intermediates in the photocycle of the Glu46Gln mutant of photoactive yellow protein: femtosecond spectroscopy.
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PDB codes: 1f5m 1fl4
10836146 Y.Z.Gu, J.B.Hogenesch, and C.A.Bradfield (2000).
The PAS superfamily: sensors of environmental and developmental signals.
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PAS domains: internal sensors of oxygen, redox potential, and light.
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The role of high-resolution structural studies in the development of commercial enzymes.
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Femtosecond spectroscopic observations of initial intermediates in the photocycle of the photoactive yellow protein from Ectothiorhodospira halophila.
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Global conformational changes upon receptor stimulation in photoactive yellow protein.
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Shedding light on the dark and weakly fluorescent states of green fluorescent proteins.
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Bacterial photoreceptor with similarity to photoactive yellow protein and plant phytochromes.
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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.
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PDB code: 1bl5
9818266 B.L.Stoddard (1998).
New results using Laue diffraction and time-resolved crystallography.
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9729742 D.Oesterhelt (1998).
The structure and mechanism of the family of retinal proteins from halophilic archaea.
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9628473 G.K.Farber (1998).
Sensing photons.
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9699613 K.Moffat (1998).
Ultrafast time-resolved crystallography.
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9753430 P.Kuhn, M.Knapp, S.M.Soltis, G.Ganshaw, M.Thoene, and R.Bott (1998).
The 0.78 A structure of a serine protease: Bacillus lentus subtilisin.
  Biochemistry, 37, 13446-13452.
PDB code: 1gci
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.
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9914254 S.Longhi, M.Czjzek, and C.Cambillau (1998).
Messages from ultrahigh resolution crystal structures.
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