Photoactive yellow protein structure

Rajagopal, S., Anderson, S., Srajer, V., Schmidt, M., Pahl, R., and Moffat K. 2005. A strnctural pathway for signaling in the Ei46Q mutant of photoactive yellow protein. Structure 13 55-63. 

Structure of the Photointermediate of Photoactive Yellow Protein and the Propagation Mechanism of Structural Change... 

Photoactive yellow protein (PYP) was discovered 20 year ago in Halorhodospira halophila, then known as Ectothiorhodospira halophila [1,2]. In several halophilic purple bacteria it has a vital role in the avoidance response to blue light (phototaxis). It has been thoroughly studied as a model photoreceptor system and as the structural prototype for the PAS class of signal transduction proteins. PYP has 125 amino acid residues in an a// -fold with six antiparallel /1-sheets and several helices (see Fig. 5.1). The covalently bound p-coumaric acid chromophore is linked to the only cysteine in the protein (Cys69) (see Fig. 5.1). Hellingwerf has published an excellent review of the photophysical behavior of PYP [1],... 

Borgstahl, G. E., D. R. Williams, et al. (1995). 1.4A structure of photoactive yellow protein, a cytosolic photoreceptor unusual fold, active site, and chromophore. Biochemistry 34(19) 6278-6287. 

Kandori, H., T. Iwata, et al. (2000). Water structural changes involved in the activation process of photoactive yellow protein. Biochemistry 39(27) 7902-7909. 

Optically induced cis-trans isomerization is a key structural dynamic element for many types of photochromic switches as stilbenes and azobenzene derivatives and for photosensor proteins as bacteriorhodopsin, rhodopsin, and photoactive yellow protein. 

Figure 4 Structure of the Bradyrhizobium japonicum FixL heme-bindiug PAS damain ( FixLH) and its close resemblance to the structure of photoactive yellow protein (PYP). On the left is a ribbons diagram showing secondary-structure elements in FixLH on the right is a comparison of the structures of FixLH (dark gray) and PYP (light gray), together with their heme and hydroxycinnamate cofactors, respectively. Consecutive letters denote consecutive regions of secondary structure. (From Ref 14.)...

PeUequer JL, Wager-Smith KA, Kay SA, Getzolf ED. Photoactive yellow protein a structural prototype for the three-dimensional fold of the PAS domain superfiunily. Proc Natl Acad Sci USA 1998 95 5884-5890. 

Figure 203 Time-resolved Infrared difference spectra of photoexcited PYP (photoactive yellow protein) measured using a step-scan FT-IR spectrometer [141. Time is indicated on a common logarithmic scale after 50 ns from photoexcitation. AAbsorbance, absorbance difference a.u., absorbance unit. (Source Reprinted by permission from Macmillan Publishers Ltd Nature Structural and Molecular Biology [14]. Copyright 2001.)...

Figure 34 CIS calculations, in a sequence of increasingly diffuse basis sets, for the phe-nolate isomer of p-coumaric acid, a chemical model of the chromophore in photoactive yellow protein. (The energy level structure of this molecule is depicted in Figure 16.) Dashed lines connect the n n transition(s) obtained in each basis, which mix with the continuum states in the more diffuse basis sets. The lowest-energy level in each basis set represents —e oMO which is the threshold energy for the onset of the continuum in the hasis-set limit. The other levels denote CIS excitation energies, most of which correspond to discretized continuum states. Adapted with permission from Ref. 187 copyright 2013 American Institute of Physics.

FIGURE 130.2 Domain structures of prokaryotic and plant phytochromes. Phytochromes have two functional domains, the JM-terminal photosensory domain and the C-terminal regulatory domain. CBD, chromophore-hearing domain HKRD, histidine kinase-related domain HKD, histidine kinase domain PAS, Pas (Per/Arndt/Sim) domain SS, serine-rich domain PYP, photoactive yellow protein domain similar to PAS domain , bilin-chromophore. (Modified from Frankhauser, C., Phytochromes as light-modulated protein kinases. Figure 1, Seminars in Cell and Developmental Biology, 11, 468, 2000. With permission from Elsevier Science.)... 

Figure 14.20 Neutron crystallographic structure of the photoactive yellow protein (PYP) [65],...

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