PDBsum entry 1t1c

Go to PDB code: 
protein ligands links
Photoreceptor PDB id
Jmol PyMol
Protein chain
125 a.a. *
* Residue conservation analysis
PDB id:
Name: Photoreceptor
Title: Late intermediate il3 from time-resolved crystallography of mutant of pyp
Structure: Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes. Mutation: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Gene: pyp. Expressed in: escherichia coli. Expression_system_taxid: 562
1.60Å     R-factor:   0.129     R-free:   0.139
Ensemble: 2 models
Authors: S.Rajagopal,S.Anderson,V.Srajer,M.Schmidt,R.Pahl,K.Moffat
Key ref:
S.Rajagopal et al. (2005). A structural pathway for signaling in the E46Q mutant of photoactive yellow protein. Structure, 13, 55-63. PubMed id: 15642261 DOI: 10.1016/j.str.2004.10.016
15-Apr-04     Release date:   18-Jan-05    
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
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to stimulus   4 terms 
  Biochemical function     photoreceptor activity     1 term  


DOI no: 10.1016/j.str.2004.10.016 Structure 13:55-63 (2005)
PubMed id: 15642261  
A structural pathway for signaling in the E46Q mutant of photoactive yellow protein.
S.Rajagopal, S.Anderson, V.Srajer, M.Schmidt, R.Pahl, K.Moffat.
In the bacterial photoreceptor photoactive yellow protein (PYP), absorption of blue light by its chromophore leads to a conformational change in the protein associated with differential signaling activity, as it executes a reversible photocycle. Time-resolved Laue crystallography allows structural snapshots (as short as 150 ps) of high crystallographic resolution (approximately 1.6 A) to be taken of a protein as it functions. Here, we analyze by singular value decomposition a comprehensive time-resolved crystallographic data set of the E46Q mutant of PYP throughout the photocycle spanning 10 ns-100 ms. We identify and refine the structures of five distinct intermediates and provide a plausible chemical kinetic mechanism for their inter conversion. A clear structural progression is visible in these intermediates, in which a signal generated at the chromophore propagates through a distinct structural pathway of conserved residues and results in structural changes near the N terminus, over 20 A distant from the chromophore.
  Selected figure(s)  
Figure 5.
Figure 5. The Chemical Kinetic Mechanism of E46Q PYP in the Crystal
(A) Chemical kinetic mechanism of E46Q PYP in the crystal, with rate coefficients (s -1) of 3.0 10^6 (IE1->IE2), 5.0 10^5 (IE2->IL1), 5.0 10^3 (IL1->IL2), 3.0 10^3 (IL1->G), 50 (IL2->IL3), and 0 (IL3->G).
(B) Predicted concentrations of IE1 (red), IE2 (magenta), IL1 (blue), IL2 (cyan), IL3 (dashed), and the ground state (black) with the mechanism in (A).
(C) Predicted concentration profiles for spectroscopic intermediates pR (IE1 and IE2) shown in red, pB (IL1 and IL2) shown in blue, and the ground state (IL3 and pG) shown in black with the mechanism in (A).
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 55-63) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19836329 A.Möglich, R.A.Ayers, and K.Moffat (2009).
Structure and signaling mechanism of Per-ARNT-Sim domains.
  Structure, 17, 1282-1294.  
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.  
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.  
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.  
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.  
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
17959373 T.De la Mora-Rey, and C.M.Wilmot (2007).
Synergy within structural biology of single crystal optical spectroscopy and X-ray crystallography.
  Curr Opin Struct Biol, 17, 580-586.  
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.  
16368695 N.Shimizu, Y.Imamoto, M.Harigai, H.Kamikubo, Y.Yamazaki, and M.Kataoka (2006).
pH-dependent equilibrium between long lived near-UV intermediates of photoactive yellow protein.
  J Biol Chem, 281, 4318-4325.  
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.  
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.  
15642256 S.Yeremenko, and K.J.Hellingwerf (2005).
Resolving protein structure dynamically.
  Structure, 13, 4-6.  
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.