PDBsum entry 1xfq

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Signaling protein PDB id
Protein chain
100 a.a. *
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Structure of the blue shifted intermediate state of the photoactive yellow protein lacking the n-terminal part
Structure: Photoactive yellow protein. Chain: a. Fragment: residues 26-125. Synonym: pyp. Engineered: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 20 models
Authors: C.Bernard,K.Houben,N.M.Derix,D.Marks,M.A.Van Der Horst, K.J.Hellingwerf,R.Boelens,R.Kaptein,N.A.Van Nuland
Key ref:
C.Bernard et al. (2005). The solution structure of a transient photoreceptor intermediate: Delta25 photoactive yellow protein. Structure, 13, 953-962. PubMed id: 16004868 DOI: 10.1016/j.str.2005.04.017
15-Sep-04     Release date:   16-Aug-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P16113  (PYP_HALHA) -  Photoactive yellow protein
125 a.a.
100 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   4 terms 
  Biochemical function     signal transducer activity     2 terms  


DOI no: 10.1016/j.str.2005.04.017 Structure 13:953-962 (2005)
PubMed id: 16004868  
The solution structure of a transient photoreceptor intermediate: Delta25 photoactive yellow protein.
C.Bernard, K.Houben, N.M.Derix, D.Marks, M.A.van der Horst, K.J.Hellingwerf, R.Boelens, R.Kaptein, N.A.van Nuland.
The N-terminally truncated variant of photoactive yellow protein (Delta25-PYP) undergoes a very similar photocycle as the corresponding wild-type protein (WT-PYP), although the lifetime of its light-illuminated (pB) state is much longer. This has allowed determination of the structure of both its dark- (pG) as well as its pB-state in solution by nuclear magnetic resonance (NMR) spectroscopy. The pG structure shows a well-defined fold, similar to WT-PYP and the X-ray structure of the pG state of Delta25-PYP. In the long-lived photocycle intermediate pB, the central beta sheet is still intact, as well as a small part of one alpha helix. The remainder of pB is unfolded and highly flexible, as evidenced by results from proton-deuterium exchange and NMR relaxation studies. Thus, the partially unfolded nature of the presumed signaling state of PYP in solution, as suggested previously, has now been structurally demonstrated.
  Selected figure(s)  
Figure 4.
Figure 4. Stereoview of the Ensemble of Solution Structures of the pG and pB States of D25-PYP
Superposition of the twenty best structures of D25-PYP in the pG (A) and the pB states (B). Structures were superimposed on the backbone atoms of the secondary structure elements, including residues 29-34, 39-41, 76-85, 89-96, 103-112, and 117-124 in the pG state, or residues 30-34, 39-41, 79-85, 90-95, 104-111, and 117-124 in the pB state. Secondary structure elements, as detected by PROCHECK, are represented and colored in blue for the b strands and red for a helices. The three flexible regions encompassing residues 43-58, 62-78, and 96-103 of pB are colored in green, wheat, and orange, respectively. For both states, the chromophore is represented in sticks. (C) Superposition of the closest to the mean structures of pG and pB. The structures were superimposed on the backbone atoms of the residues involved in the b sheet in the pB state (30-34, 39-41, 90-95, 104-112, and 117-124). pG and pB are colored in yellow and blue, respectively. The chromophore is represented by sticks.
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 953-962) copyright 2005.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  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.  
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.  
20102599 M.Krzeminski, K.Loth, R.Boelens, and A.M.Bonvin (2010).
SAMPLEX: automatic mapping of perturbed and unperturbed regions of proteins and complexes.
  BMC Bioinformatics, 11, 51.  
20835493 S.A.Morgan, and G.A.Woolley (2010).
A photoswitchable DNA-binding protein based on a truncated GCN4-photoactive yellow protein chimera.
  Photochem Photobiol Sci, 9, 1320-1326.  
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.  
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.  
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
18024503 Y.Hoshihara, Y.Imamoto, M.Kataoka, F.Tokunaga, and M.Terazima (2008).
Conformational changes in the N-terminal region of photoactive yellow protein: a time-resolved diffusion study.
  Biophys J, 94, 2187-2193.  
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.  
18227128 Y.Imamoto, S.Tatsumi, M.Harigai, Y.Yamazaki, H.Kamikubo, and M.Kataoka (2008).
Diverse roles of glycine residues conserved in photoactive yellow proteins.
  Biophys J, 94, 3620-3628.  
17510367 B.D.Zoltowski, C.Schwerdtfeger, J.Widom, J.J.Loros, A.M.Bilwes, J.C.Dunlap, and B.R.Crane (2007).
Conformational switching in the fungal light sensor Vivid.
  Science, 316, 1054-1057.
PDB codes: 2pd7 2pd8 2pdr 2pdt
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.  
17373703 K.Shirai, Y.Yamazaki, H.Kamikubo, Y.Imamoto, and M.Kataoka (2007).
Attempt to simplify the amino-acid sequence of photoactive yellow protein with a set of simple rules.
  Proteins, 67, 821-833.  
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.  
16323221 J.S.Grinstead, S.T.Hsu, W.Laan, A.M.Bonvin, K.J.Hellingwerf, R.Boelens, and R.Kaptein (2006).
The solution structure of the AppA BLUF domain: insight into the mechanism of light-induced signaling.
  Chembiochem, 7, 187-193.
PDB code: 2bun
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.  
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.  
16331422 G.Fuentes, A.J.Nederveen, R.Kaptein, R.Boelens, and A.M.Bonvin (2005).
Describing partially unfolded states of proteins from sparse NMR data.
  J Biomol NMR, 33, 175-186.  
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.