PDBsum entry 1s1z

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Photoreceptor PDB id
Protein chain
125 a.a. *
Waters ×106
* Residue conservation analysis
PDB id:
Name: Photoreceptor
Title: Photoactivated chromophore conformation in photoactive yellow protein (e46q mutant) from 10 to 500 nanoseconds
Structure: Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes. Mutation: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Expressed in: escherichia coli. Expression_system_taxid: 562
1.60Å     R-factor:   0.053     R-free:   0.060
Authors: S.Anderson,V.Srajer,R.Pahl,S.Rajagopal,F.Schotte,P.Anfinrud, M.Wulff,K.Moffat
Key ref:
S.Anderson et al. (2004). Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein. Structure, 12, 1039-1045. PubMed id: 15274923 DOI: 10.1016/j.str.2004.04.008
07-Jan-04     Release date:   15-Jun-04    
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   5 terms 
  Biochemical function     signal transducer activity     2 terms  


DOI no: 10.1016/j.str.2004.04.008 Structure 12:1039-1045 (2004)
PubMed id: 15274923  
Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein.
S.Anderson, V.Srajer, R.Pahl, S.Rajagopal, F.Schotte, P.Anfinrud, M.Wulff, K.Moffat.
We use time-resolved crystallography to observe the structural progression of a bacterial blue light photoreceptor throughout its photocycle. Data were collected from 10 ns to 100 ms after photoactivation of the E46Q mutant of photoactive yellow protein. Refinement of transient chromophore conformations shows that the spectroscopically distinct intermediates are formed via progressive disruption of the hydrogen bond network to the chromophore. Although structural change occurs within a few nanoseconds on and around the chromophore, it takes milliseconds for a distinct pattern of tertiary structural change to fully progress through the entire molecule, thus generating the putative signaling state. Remarkably, the coupling between the chromophore conformation and the tertiary structure of this small protein is not tight: there are leads and lags between changes in the conformation of the chromophore and the protein tertiary structure.
  Selected figure(s)  
Figure 5.
Figure 5. Chromophore Conformations in the pR and pB IntermediatesDifference electron density maps (A and B) and electron density maps (C and D) for the pR and pB chromophore conformations, derived from the two highly averaged data sets (Table 2). Difference electron density contoured at ▒2s and ▒3.5s, for the (A) pR and (B) pB states. Electron density maps contoured at ▒1s and ▒3s; yellow atomic model, ground-state conformation; orange models, chromophore conformations for the (C) pR and (D) pB states.
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1039-1045) copyright 2004.  
  Figure was 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.  
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.  
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.  
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.  
19130540 M.Chergui, and A.H.Zewail (2009).
Electron and X-ray methods of ultrafast structural dynamics: advances and applications.
  Chemphyschem, 10, 28-43.  
19240329 R.L.Owen, A.R.Pearson, A.Meents, P.Boehler, V.Thominet, and C.Schulze-Briese (2009).
A new on-axis multimode spectrometer for the macromolecular crystallography beamlines of the Swiss Light Source.
  J Synchrotron Radiat, 16, 173-182.  
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.  
16121278 M.A.van der Horst, W.Laan, S.Yeremenko, A.Wende, P.Palm, D.Oesterhelt, and K.J.Hellingwerf (2005).
From primary photochemistry to biological function in the blue-light photoreceptors PYP and AppA.
  Photochem Photobiol Sci, 4, 688-693.  
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.  
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 codes are shown on the right.