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PDBsum entry 1ts6

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Photoreceptor PDB id
1ts6
Jmol
Contents
Protein chain
125 a.a. *
Ligands
HC4
* Residue conservation analysis
PDB id:
1ts6
Name: Photoreceptor
Title: Structure of the pb2 intermediate from time-resolved laue crystallography
Structure: Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Gene: pyp. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.60Å     R-factor:   0.181     R-free:   0.186
Ensemble: 2 models
Authors: H.Ihee,S.Rajagopal,V.Srajer,R.Pahl,S.Anderson,M.Schmidt, F.Schotte,P.A.Anfinrud,M.Wulff,K.Moffat
Key ref:
H.Ihee et al. (2005). Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds. Proc Natl Acad Sci U S A, 102, 7145-7150. PubMed id: 15870207 DOI: 10.1073/pnas.0409035102
Date:
21-Jun-04     Release date:   05-Jul-05    
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: 10.1073/pnas.0409035102 Proc Natl Acad Sci U S A 102:7145-7150 (2005)
PubMed id: 15870207  
 
 
Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.
H.Ihee, S.Rajagopal, V.Srajer, R.Pahl, S.Anderson, M.Schmidt, F.Schotte, P.A.Anfinrud, M.Wulff, K.Moffat.
 
  ABSTRACT  
 
Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (PYP) from Halorhodospira halophila. By analyzing a comprehensive set of Laue data during the PYP photocycle (forty-seven time points from one nanosecond to one second), we track all atoms in PYP during its photocycle and directly observe how absorption of a blue light photon by its p-coumaric acid chromophore triggers a reversible photocycle. We identify a complex chemical mechanism characterized by five distinct structural intermediates. Structural changes at the chromophore in the early, red-shifted intermediates are transduced to the exterior of the protein in the late, blue-shifted intermediates through an initial "volume-conserving" isomerization of the chromophore and the progressive disruption of hydrogen bonds between the chromophore and its surrounding binding pocket. These results yield a comprehensive view of the PYP photocycle when seen in the light of previous biophysical studies on the system.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Chromophore-binding pocket views of refined intermediate structures and mechanism for the isomerization and rotation of the pCA chromophore upon absorption of blue light. Five distinct structural intermediates (I[CP], pR[CW], pR[E46Q], pB[1], and pB[2]) were identified from four chemical states ( , , , and ) shown in Fig. 2. I[CP] is shown twice to demonstrate the biphasic pathways to pR[CW] and pR[E46Q]. Isomerization and rotation about single bonds are shown by arrows; hydrogen bonds are dotted. A bicycle pedal mechanism (44), which couples trans-cis isomerization of the C2 C3 double bond with rotation about a nonadjacent single bond, is used for the dark state to I[CP] transition. Further rotations about single bonds result in the pB[1] conformation. pB[2] reverts thermally to the dark state with no further detectable intermediates.
Figure 4.
Fig. 4. Properties of the chemical kinetic mechanism of the wild-type PYP photocycle. (A) General chemical kinetic mechanism used to fit the data. The dashed arrow indicates the light-driven reaction from pG to the first intermediate observed here, I[CP]. (B) Predicted concentrations of intermediates [I[CP] (red), pR[CW] (magenta), pR[E46Q] (purple), pB[1] (blue), pB[2] (cyan), and the dark state (black)] after posterior analysis with rate coefficients (s-1): k[1] = 4.8 x 10^7; k[2] = 3.7 x 10^7; k[3] = 3.0 x 10^3; k[4] = 3.3 x 10^4; k[5] = 55; k[6] = 100; and k[7] = 7.1. The seven rate coefficients correspond to time constants of 21 ns, 27 ns, 333 µs, 30 µs, 18 ms, 10 ms, and 141 ms, respectively.
 
  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.  
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.  
20055677 C.Bressler, and M.Chergui (2010).
Molecular structural dynamics probed by ultrafast X-ray absorption spectroscopy.
  Annu Rev Phys Chem, 61, 263-282.  
  20953237 E.C.Carroll, S.H.Song, M.Kumauchi, I.H.van Stokkum, A.Jailaubekov, W.D.Hoff, and D.S.Larsen (2010).
Subpicosecond Excited-State Proton Transfer Preceding Isomerization During the Photorecovery of Photoactive Yellow Protein.
  J Phys Chem Lett, 1, 2793-2799.  
20133629 G.Hummer (2010).
Catching a protein in the act.
  Proc Natl Acad Sci U S A, 107, 2381-2382.  
20164650 J.Kim, K.H.Kim, J.H.Lee, and H.Ihee (2010).
Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospects.
  Acta Crystallogr A, 66, 270-280.  
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.  
20164646 M.Chergui (2010).
Picosecond and femtosecond X-ray absorption spectroscopy of molecular systems.
  Acta Crystallogr A, 66, 229-239.  
20164643 M.Schmidt, T.Graber, R.Henning, and V.Srajer (2010).
Five-dimensional crystallography.
  Acta Crystallogr A, 66, 198-206.  
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.  
20820568 T.Hoyer, W.Tuszynski, and C.Lienau (2010).
Competing ultrafast photoinduced quenching reactions in cinnamic acid : peptide blends.
  Phys Chem Chem Phys, 12, 13052-13060.  
20119482 A.Specht, F.Bolze, Z.Omran, J.F.Nicoud, and M.Goeldner (2009).
Photochemical tools to study dynamic biological processes.
  HFSP J, 3, 255-264.  
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.  
19585639 T.K.Kim, J.H.Lee, M.Wulff, Q.Kong, and H.Ihee (2009).
Spatiotemporal kinetics in solution studied by time-resolved X-ray liquidography (solution scattering).
  Chemphyschem, 10, 1958-1980.  
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.  
18309395 K.Koike, K.Kawaguchi, and T.Yamato (2008).
Stress tensor analysis of the protein quake of photoactive yellow protein.
  Phys Chem Chem Phys, 10, 1400-1405.  
18184580 M.Andersson, J.Vincent, D.van der Spoel, J.Davidsson, and R.Neutze (2008).
A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins.
  Structure, 16, 21-28.  
18806790 M.Cammarata, M.Levantino, F.Schotte, P.A.Anfinrud, F.Ewald, J.Choi, A.Cupane, M.Wulff, and H.Ihee (2008).
Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering.
  Nat Methods, 5, 881-886.  
18380006 M.Milani, M.Nardini, A.Pesce, E.Mastrangelo, and M.Bolognesi (2008).
Hemoprotein time-resolved X-ray crystallography.
  IUBMB Life, 60, 154-158.  
19436491 P.Ormos (2008).
Dynamic fluctuation of proteins watched in real time.
  HFSP J, 2, 297-301.  
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.  
17914477 D.Bourgeois, F.Schotte, M.Brunori, and B.Vallone (2007).
Time-resolved methods in biophysics. 6. Time-resolved Laue crystallography as a tool to investigate photo-activated protein dynamics.
  Photochem Photobiol Sci, 6, 1047-1056.  
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.  
17677998 M.Braun, C.Korff Schmising, M.Kiel, N.Zhavoronkov, J.Dreyer, M.Bargheer, T.Elsaesser, C.Root, T.E.Schrader, P.Gilch, W.Zinth, and M.Woerner (2007).
Ultrafast changes of molecular crystal structure induced by dipole solvation.
  Phys Rev Lett, 98, 248301.  
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
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.  
16547137 D.Bourgeois, B.Vallone, A.Arcovito, G.Sciara, F.Schotte, P.A.Anfinrud, and M.Brunori (2006).
Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography.
  Proc Natl Acad Sci U S A, 103, 4924-4929.  
16684887 J.E.Knapp, R.Pahl, V.Srajer, and W.E.Royer (2006).
Allosteric action in real time: time-resolved crystallographic studies of a cooperative dimeric hemoglobin.
  Proc Natl Acad Sci U S A, 103, 7649-7654.
PDB codes: 2grf 2grh 2grz
17100451 J.H.Lee, K.H.Kim, T.K.Kim, Y.Lee, and H.Ihee (2006).
Analyzing solution-phase time-resolved x-ray diffraction data by isolated-solute models.
  J Chem Phys, 125, 174504.  
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.  
16599694 M.Cammarata, M.Lorenc, T.K.Kim, J.H.Lee, Q.Y.Kong, E.Pontecorvo, M.Lo Russo, G.Schiró, A.Cupane, M.Wulff, and H.Ihee (2006).
Impulsive solvent heating probed by picosecond x-ray diffraction.
  J Chem Phys, 124, 124504.  
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.  
16129597 D.Bourgeois, and A.Royant (2005).
Advances in kinetic protein crystallography.
  Curr Opin Struct Biol, 15, 538-547.  
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.  
16109869 P.Anfinrud, and F.Schotte (2005).
Chemistry. X-ray fingerprinting of chemical intermediates in solution.
  Science, 309, 1192-1193.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.