PDBsum entry 1f9i

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Signaling protein PDB id
Jmol PyMol
Protein chain
125 a.a. *
Waters ×104
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Crystal structure of the photoactive yellow protein mutant y42f
Structure: Photoactive yellow protein. Chain: a. Engineered: yes. Mutation: yes
Source: Halorhodospira halophila. Organism_taxid: 1053. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.10Å     R-factor:   0.146     R-free:   0.171
Authors: R.Brudler,T.E.Meyer,U.K.Genick,G.Tollin,E.D.Getzoff
Key ref:
R.Brudler et al. (2000). Coupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein. Biochemistry, 39, 13478-13486. PubMed id: 11063584 DOI: 10.1021/bi0009946
10-Jul-00     Release date:   21-Jul-00    
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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: 10.1021/bi0009946 Biochemistry 39:13478-13486 (2000)
PubMed id: 11063584  
Coupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein.
R.Brudler, T.E.Meyer, U.K.Genick, S.Devanathan, T.T.Woo, D.P.Millar, K.Gerwert, M.A.Cusanovich, G.Tollin, E.D.Getzoff.
To understand in atomic detail how a chromophore and a protein interact to sense light and send a biological signal, we are characterizing photoactive yellow protein (PYP), a water-soluble, 14 kDa blue-light receptor which undergoes a photocycle upon illumination. The active site residues glutamic acid 46, arginine 52, tyrosine 42, and threonine 50 form a hydrogen bond network with the anionic p-hydroxycinnamoyl cysteine 69 chromophore in the PYP ground state, suggesting an essential role for these residues for the maintenance of the chromophore's negative charge, the photocycle kinetics, the signaling mechanism, and the protein stability. Here, we describe the role of T50 and Y42 by use of site-specific mutants. T50 and Y42 are involved in fine-tuning the chromophore's absorption maximum. The high-resolution X-ray structures show that the hydrogen-bonding interactions between the protein and the chromophore are weakened in the mutants, leading to increased electron density on the chromophore's aromatic ring and consequently to a red shift of its absorption maximum from 446 nm to 457 and 458 nm in the mutants T50V and Y42F, respectively. Both mutants have slightly perturbed photocycle kinetics and, similar to the R52A mutant, are bleached more rapidly and recover more slowly than the wild type. The effect of pH on the kinetics is similar to wild-type PYP, suggesting that T50 and Y42 are not directly involved in any protonation or deprotonation events that control the speed of the light cycle. The unfolding energies, 26.8 and 25.1 kJ/mol for T50V and Y42F, respectively, are decreased when compared to that of the wild type (29.7 kJ/mol). In the mutant Y42F, the reduced protein stability gives rise to a second PYP population with an altered chromophore conformation as shown by UV/visible and FT Raman spectroscopy. The second chromophore conformation gives rise to a shoulder at 391 nm in the UV/visible absorption spectrum and indicates that the hydrogen bond between Y42 and the chromophore is crucial for the stabilization of the native chromophore and protein conformation. The two conformations in the Y42F mutant can be interconverted by chaotropic and kosmotropic agents, respectively, according to the Hofmeister series. The FT Raman spectra and the acid titration curves suggest that the 391 nm form of the chromophore is not fully protonated. The fluorescence quantum yield of the mutant Y42F is 1.8% and is increased by an order of magnitude when compared to the wild type.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21301710 C.Loukou, P.Changenet-Barret, M.N.Rager, P.Plaza, M.M.Martin, and J.M.Mallet (2011).
The design, synthesis and photochemical study of a biomimetic cyclodextrin model of photoactive yellow protein (PYP).
  Org Biomol Chem, 9, 2209-2218.  
19707683 K.Okamoto, N.Hamada, T.A.Okamura, N.Ueyama, and H.Yamamoto (2009).
Color regulation and stabilization of chromophore by Cys69 in photoactive yellow protein active center.
  Org Biomol Chem, 7, 3782-3791.  
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.  
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.  
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.  
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.  
16709144 H.Yamada, M.Kumauchi, N.Hamada, X.G.Zheng, I.H.Park, K.Masuda, K.Yoshihara, and F.Tokunaga (2006).
Analogue chromophore study of the influence of electronic perturbation on color regulation of photoactive yellow protein.
  Photochem Photobiol, 82, 1422-1425.  
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.  
15009198 M.H.Hefti, K.J.Françoijs, 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.  
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
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
15274923 S.Anderson, V.Srajer, R.Pahl, S.Rajagopal, F.Schotte, P.Anfinrud, M.Wulff, and K.Moffat (2004).
Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein.
  Structure, 12, 1039-1045.
PDB codes: 1s1y 1s1z
12496261 A.Haker, J.Hendriks, I.H.van Stokkum, J.Heberle, K.J.Hellingwerf, W.Crielaard, and T.Gensch (2003).
The two photocycles of photoactive yellow protein from Rhodobacter sphaeroides.
  J Biol Chem, 278, 8442-8451.  
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
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.  
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.  
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.  
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.  
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.