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Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion.

Yang X, Stojkovic EA, Kuk J, Moffat K
Proc Natl Acad Sci U S A 104 12571-6 (2007)
Cited: 126 times
EuropePMC logo PMID: 17640891

Abstract

Bacteriophytochromes RpBphP2 and RpBphP3 from the photosynthetic bacterium Rhodopseudomonas palustris work in tandem to modulate synthesis of the light-harvesting complex LH4 in response to light. Although RpBphP2 and RpBphP3 share the same domain structure with 52% sequence identity, they demonstrate distinct photoconversion behaviors. RpBphP2 exhibits the "classical" phytochrome behavior of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states, whereas RpBphP3 exhibits novel photoconversion between Pr and a near-red (Pnr) light-absorbing states. We have determined the crystal structure at 2.2-A resolution of the chromophore binding domains of RpBphP3, covalently bound with chromophore biliverdin IXalpha. By combining structural and sequence analyses with site-directed mutagenesis, we identify key residues that directly modulate the photochemical properties of RpBphP3 and RpBphP2. Remarkably, we identify a region spanning residues 207-212 in RpBphP3, in which a single mutation, L207Y, causes this unusual bacteriophytochrome to revert to the classical phenotype that undergoes reversible photoconversion between the Pr and Pfr states. The reverse mutation, Y193L, in the corresponding region in RpBphP2 significantly diminishes the formation of the Pfr state. We propose that residues 207-212 and the spatially adjacent conserved residues, Asp-216 and Tyr-272, interact with the chromophore and form part of the interface between the chromophore binding domains and the PHY domain that modulates photoconversion.

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  1. Structure and signaling mechanism of Per-ARNT-Sim domains. Möglich A, Ayers RA, Moffat K. Structure 17 1282-1294 (2009)
  2. PAS domains in bacterial signal transduction. Stuffle EC, Johnson MS, Watts KJ. Curr Opin Microbiol 61 8-15 (2021)
  3. Phytochromes in Agrobacterium fabrum. Lamparter T, Xue P, Elkurdi A, Kaeser G, Sauthof L, Scheerer P, Krauß N. Front Plant Sci 12 642801 (2021)

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  1. Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction. Yang X, Kuk J, Moffat K. Proc Natl Acad Sci U S A 105 14715-14720 (2008)
  2. Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion. Yang X, Stojkovic EA, Kuk J, Moffat K. Proc Natl Acad Sci U S A 104 12571-12576 (2007)
  3. Conservation of complex knotting and slipknotting patterns in proteins. Sułkowska JI, Rawdon EJ, Millett KC, Onuchic JN, Stasiak A. Proc Natl Acad Sci U S A 109 E1715-23 (2012)
  4. Proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome. Toh KC, Stojkovic EA, van Stokkum IH, Moffat K, Kennis JT. Proc Natl Acad Sci U S A 107 9170-9175 (2010)
  5. O2- and NO-sensing mechanism through the DevSR two-component system in Mycobacterium smegmatis. Lee JM, Cho HY, Cho HJ, Ko IJ, Park SW, Baik HS, Oh JH, Eom CY, Kim YM, Kang BS, Oh JI. J Bacteriol 190 6795-6804 (2008)
  6. Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state. Cornilescu G, Ulijasz AT, Cornilescu CC, Markley JL, Vierstra RD. J Mol Biol 383 403-413 (2008)
  7. Light Signaling Mechanism of Two Tandem Bacteriophytochromes. Yang X, Stojković EA, Ozarowski WB, Kuk J, Davydova E, Moffat K. Structure 23 1179-1189 (2015)
  8. Bright blue-shifted fluorescent proteins with Cys in the GAF domain engineered from bacterial phytochromes: fluorescence mechanisms and excited-state dynamics. Hontani Y, Shcherbakova DM, Baloban M, Zhu J, Verkhusha VV, Kennis JT. Sci Rep 6 37362 (2016)
  9. The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition. Krieger IV, Kuznetsov V, Chang JY, Zhang J, Moussa SH, Young RF, Sacchettini JC. J Mol Biol 432 4623-4636 (2020)
  10. Crystallization and preliminary X-ray studies of the chromophore-binding domain of cyanobacteriochrome AnPixJ from Anabaena sp. PCC 7120. Narikawa R, Muraki N, Shiba T, Ikeuchi M, Kurisu G. Acta Crystallogr Sect F Struct Biol Cryst Commun 65 159-162 (2009)
  11. A conserved helical capping hydrogen bond in PAS domains controls signaling kinetics in the superfamily prototype photoactive yellow protein. Kumauchi M, Kaledhonkar S, Philip AF, Wycoff J, Hara M, Li Y, Xie A, Hoff WD. J Am Chem Soc 132 15820-15830 (2010)
  12. Phylogenetic Analysis with Prediction of Cofactor or Ligand Binding for Pseudomonas aeruginosa PAS and Cache Domains. Hutchin A, Cordery C, Walsh MA, Webb JS, Tews I. Microbiol Spectr 9 e0102621 (2021)


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  1. Structure and function of plant photoreceptors. Möglich A, Yang X, Ayers RA, Moffat K. Annu Rev Plant Biol 61 21-47 (2010)
  2. A brief history of phytochromes. Rockwell NC, Lagarias JC. Chemphyschem 11 1172-1180 (2010)
  3. Cyanobacteriochromes: a new superfamily of tetrapyrrole-binding photoreceptors in cyanobacteria. Ikeuchi M, Ishizuka T. Photochem Photobiol Sci 7 1159-1167 (2008)
  4. Sensor domains of two-component regulatory systems. Cheung J, Hendrickson WA. Curr Opin Microbiol 13 116-123 (2010)
  5. Bacterial phytochromes: more than meets the light. Auldridge ME, Forest KT. Crit Rev Biochem Mol Biol 46 67-88 (2011)
  6. Phytochromes: an atomic perspective on photoactivation and signaling. Burgie ES, Vierstra RD. Plant Cell 26 4568-4583 (2014)
  7. Engineering of bacterial phytochromes for near-infrared imaging, sensing, and light-control in mammals. Piatkevich KD, Subach FV, Verkhusha VV. Chem Soc Rev 42 3441-3452 (2013)
  8. Photosensing in chemotrophic, non-phototrophic bacteria: let there be light sensing too. van der Horst MA, Key J, Hellingwerf KJ. Trends Microbiol 15 554-562 (2007)
  9. Old chromophores, new photoactivation paradigms, trendy applications: flavins in blue light-sensing photoreceptors. Losi A, Gärtner W. Photochem Photobiol 87 491-510 (2011)
  10. Evolutionary studies illuminate the structural-functional model of plant phytochromes. Mathews S. Plant Cell 22 4-16 (2010)
  11. Phytochrome cytoplasmic signaling. Hughes J. Annu Rev Plant Biol 64 377-402 (2013)
  12. Bacteriophytochromes in anoxygenic photosynthetic bacteria. Giraud E, Verméglio A. Photosynth Res 97 141-153 (2008)
  13. Photoreceptor engineering. Ziegler T, Möglich A. Front Mol Biosci 2 30 (2015)
  14. The phytochrome red/far-red photoreceptor superfamily. Sharrock RA. Genome Biol 9 230 (2008)
  15. Subsystem-based theoretical spectroscopy of biomolecules and biomolecular assemblies. Neugebauer J. Chemphyschem 10 3148-3173 (2009)
  16. Circadian oscillator proteins across the kingdoms of life: structural aspects. Saini R, Jaskolski M, Davis SJ. BMC Biol 17 13 (2019)
  17. Light-induced conformational changes of the chromophore and the protein in phytochromes: bacterial phytochromes as model systems. Scheerer P, Michael N, Park JH, Nagano S, Choe HW, Inomata K, Borucki B, Krauss N, Lamparter T. Chemphyschem 11 1090-1105 (2010)
  18. Solid-state NMR spectroscopy to probe photoactivation in canonical phytochromes. Song C, Rohmer T, Tiersch M, Zaanen J, Hughes J, Matysik J. Photochem Photobiol 89 259-273 (2013)
  19. Bacteriophytochromes - from informative model systems of phytochrome function to powerful tools in cell biology. Gourinchas G, Etzl S, Winkler A. Curr Opin Struct Biol 57 72-83 (2019)
  20. From photon to signal in phytochromes: similarities and differences between prokaryotic and plant phytochromes. Nagano S. J Plant Res 129 123-135 (2016)
  21. Multistep Signaling in Nature: A Close-Up of Geobacter Chemotaxis Sensing. Silva MA, Salgueiro CA. Int J Mol Sci 22 9034 (2021)
  22. Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives. Ohlendorf R, Möglich A. Front Bioeng Biotechnol 10 1029403 (2022)
  23. Vibrational Spectroscopy of Phytochromes. Hildebrandt P. Biomolecules 13 1007 (2023)

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  1. The structure of a complete phytochrome sensory module in the Pr ground state. Essen LO, Mailliet J, Hughes J. Proc Natl Acad Sci U S A 105 14709-14714 (2008)
  2. Mutational analysis of Deinococcus radiodurans bacteriophytochrome reveals key amino acids necessary for the photochromicity and proton exchange cycle of phytochromes. Wagner JR, Zhang J, von Stetten D, Günther M, Murgida DH, Mroginski MA, Walker JM, Forest KT, Hildebrandt P, Vierstra RD. J Biol Chem 283 12212-12226 (2008)
  3. Cyanobacteriochrome CcaS is the green light receptor that induces the expression of phycobilisome linker protein. Hirose Y, Shimada T, Narikawa R, Katayama M, Ikeuchi M. Proc Natl Acad Sci U S A 105 9528-9533 (2008)
  4. Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome. Yang X, Ren Z, Kuk J, Moffat K. Nature 479 428-432 (2011)
  5. Two ground state isoforms and a chromophore D-ring photoflip triggering extensive intramolecular changes in a canonical phytochrome. Song C, Psakis G, Lang C, Mailliet J, Gärtner W, Hughes J, Matysik J. Proc Natl Acad Sci U S A 108 3842-3847 (2011)
  6. Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome. Yang X, Kuk J, Moffat K. Proc Natl Acad Sci U S A 106 15639-15644 (2009)
  7. Eukaryotic algal phytochromes span the visible spectrum. Rockwell NC, Duanmu D, Martin SS, Bachy C, Price DC, Bhattacharya D, Worden AZ, Lagarias JC. Proc Natl Acad Sci U S A 111 3871-3876 (2014)
  8. Structures of cyanobacteriochromes from phototaxis regulators AnPixJ and TePixJ reveal general and specific photoconversion mechanism. Narikawa R, Ishizuka T, Muraki N, Shiba T, Kurisu G, Ikeuchi M. Proc Natl Acad Sci U S A 110 918-923 (2013)
  9. A novel photoactive GAF domain of cyanobacteriochrome AnPixJ that shows reversible green/red photoconversion. Narikawa R, Fukushima Y, Ishizuka T, Itoh S, Ikeuchi M. J Mol Biol 380 844-855 (2008)
  10. A second conserved GAF domain cysteine is required for the blue/green photoreversibility of cyanobacteriochrome Tlr0924 from Thermosynechococcus elongatus. Rockwell NC, Njuguna SL, Roberts L, Castillo E, Parson VL, Dwojak S, Lagarias JC, Spiller SC. Biochemistry 47 7304-7316 (2008)
  11. Structural basis for the photoconversion of a phytochrome to the activated Pfr form. Ulijasz AT, Cornilescu G, Cornilescu CC, Zhang J, Rivera M, Markley JL, Vierstra RD. Nature 463 250-254 (2010)
  12. Structure-guided engineering enhances a phytochrome-based infrared fluorescent protein. Auldridge ME, Satyshur KA, Anstrom DM, Forest KT. J Biol Chem 287 7000-7009 (2012)
  13. Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor. Clack T, Shokry A, Moffet M, Liu P, Faul M, Sharrock RA. Plant Cell 21 786-799 (2009)
  14. Distinct classes of red/far-red photochemistry within the phytochrome superfamily. Rockwell NC, Shang L, Martin SS, Lagarias JC. Proc Natl Acad Sci U S A 106 6123-6127 (2009)
  15. Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor. Bellini D, Papiz MZ. Structure 20 1436-1446 (2012)
  16. A photo-labile thioether linkage to phycoviolobilin provides the foundation for the blue/green photocycles in DXCF-cyanobacteriochromes. Burgie ES, Walker JM, Phillips GN, Vierstra RD. Structure 21 88-97 (2013)
  17. Light-induced chromophore activity and signal transduction in phytochromes observed by 13C and 15N magic-angle spinning NMR. Rohmer T, Lang C, Hughes J, Essen LO, Gärtner W, Matysik J. Proc Natl Acad Sci U S A 105 15229-15234 (2008)
  18. Crystallographic and electron microscopic analyses of a bacterial phytochrome reveal local and global rearrangements during photoconversion. Burgie ES, Wang T, Bussell AN, Walker JM, Li H, Vierstra RD. J Biol Chem 289 24573-24587 (2014)
  19. Fluorescence quantum yield and photochemistry of bacteriophytochrome constructs. Toh KC, Stojković EA, van Stokkum IH, Moffat K, Kennis JT. Phys Chem Chem Phys 13 11985-11997 (2011)
  20. Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy. Li H, Zhang J, Vierstra RD, Li H. Proc Natl Acad Sci U S A 107 10872-10877 (2010)
  21. Cyanochromes are blue/green light photoreversible photoreceptors defined by a stable double cysteine linkage to a phycoviolobilin-type chromophore. Ulijasz AT, Cornilescu G, von Stetten D, Cornilescu C, Velazquez Escobar F, Zhang J, Stankey RJ, Rivera M, Hildebrandt P, Vierstra RD. J Biol Chem 284 29757-29772 (2009)
  22. Photophysical diversity of two novel cyanobacteriochromes with phycocyanobilin chromophores: photochemistry and dark reversion kinetics. Chen Y, Zhang J, Luo J, Tu JM, Zeng XL, Xie J, Zhou M, Zhao JQ, Scheer H, Zhao KH. FEBS J 279 40-54 (2012)
  23. Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo. Li L, Shemetov AA, Baloban M, Hu P, Zhu L, Shcherbakova DM, Zhang R, Shi J, Yao J, Wang LV, Verkhusha VV. Nat Commun 9 2734 (2018)
  24. Characterization of two thermostable cyanobacterial phytochromes reveals global movements in the chromophore-binding domain during photoconversion. Ulijasz AT, Cornilescu G, von Stetten D, Kaminski S, Mroginski MA, Zhang J, Bhaya D, Hildebrandt P, Vierstra RD. J Biol Chem 283 21251-21266 (2008)
  25. Origins of fluorescence in evolved bacteriophytochromes. Bhattacharya S, Auldridge ME, Lehtivuori H, Ihalainen JA, Forest KT. J Biol Chem 289 32144-32152 (2014)
  26. Dynamic structural changes underpin photoconversion of a blue/green cyanobacteriochrome between its dark and photoactivated states. Cornilescu CC, Cornilescu G, Burgie ES, Markley JL, Ulijasz AT, Vierstra RD. J Biol Chem 289 3055-3065 (2014)
  27. Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: reconciling structural and spectroscopic data by QM/MM calculations. Mroginski MA, von Stetten D, Escobar FV, Strauss HM, Kaminski S, Scheerer P, Günther M, Murgida DH, Schmieder P, Bongards C, Gärtner W, Mailliet J, Hughes J, Essen LO, Hildebrandt P. Biophys J 96 4153-4163 (2009)
  28. Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes. Salewski J, Escobar FV, Kaminski S, von Stetten D, Keidel A, Rippers Y, Michael N, Scheerer P, Piwowarski P, Bartl F, Frankenberg-Dinkel N, Ringsdorf S, Gärtner W, Lamparter T, Mroginski MA, Hildebrandt P. J Biol Chem 288 16800-16814 (2013)
  29. A protonation-coupled feedback mechanism controls the signalling process in bathy phytochromes. Velazquez Escobar F, Piwowarski P, Salewski J, Michael N, Fernandez Lopez M, Rupp A, Qureshi BM, Scheerer P, Bartl F, Frankenberg-Dinkel N, Siebert F, Andrea Mroginski M, Hildebrandt P. Nat Chem 7 423-430 (2015)
  30. Characterization of the photoactive GAF domain of the CikA homolog (SyCikA, Slr1969) of the cyanobacterium Synechocystis sp. PCC 6803. Narikawa R, Kohchi T, Ikeuchi M. Photochem Photobiol Sci 7 1253-1259 (2008)
  31. Structure-guided engineering of plant phytochrome B with altered photochemistry and light signaling. Zhang J, Stankey RJ, Vierstra RD. Plant Physiol 161 1445-1457 (2013)
  32. The D-ring, not the A-ring, rotates in Synechococcus OS-B' phytochrome. Song C, Psakis G, Psakis G, Kopycki J, Lang C, Matysik J, Hughes J. J Biol Chem 289 2552-2562 (2014)
  33. Asymmetric activation mechanism of a homodimeric red light-regulated photoreceptor. Gourinchas G, Heintz U, Winkler A. Elife 7 e34815 (2018)
  34. Chromophore heterogeneity and photoconversion in phytochrome crystals and solution studied by resonance Raman spectroscopy. von Stetten D, Günther M, Scheerer P, Murgida DH, Mroginski MA, Krauss N, Lamparter T, Zhang J, Anstrom DM, Vierstra RD, Forest KT, Hildebrandt P. Angew Chem Int Ed Engl 47 4753-4755 (2008)
  35. Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies. Baloban M, Shcherbakova DM, Pletnev S, Pletnev VZ, Lagarias JC, Verkhusha VV. Chem Sci 8 4546-4557 (2017)
  36. FTIR Spectroscopy Revealing Light-Dependent Refolding of the Conserved Tongue Region of Bacteriophytochrome. Stojković EA, Toh KC, Alexandre MT, Baclayon M, Moffat K, Kennis JT. J Phys Chem Lett 5 2512-2515 (2014)
  37. Dimerization properties of the RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis. Bellini D, Papiz MZ. Acta Crystallogr D Biol Crystallogr 68 1058-1066 (2012)
  38. Unusual spectral properties of bacteriophytochrome Agp2 result from a deprotonation of the chromophore in the red-absorbing form Pr. Zienicke B, Molina I, Glenz R, Singer P, Ehmer D, Escobar FV, Hildebrandt P, Diller R, Lamparter T. J Biol Chem 288 31738-31751 (2013)
  39. Light-induced activation of bacterial phytochrome Agp1 monitored by static and time-resolved FTIR spectroscopy. Piwowarski P, Ritter E, Hofmann KP, Hildebrandt P, von Stetten D, Scheerer P, Michael N, Lamparter T, Bartl F. Chemphyschem 11 1207-1214 (2010)
  40. Locked 5Zs-biliverdin blocks the Meta-RA to Meta-RC transition in the functional cycle of bacteriophytochrome Agp1. Seibeck S, Borucki B, Otto H, Inomata K, Khawn H, Kinoshita H, Michael N, Lamparter T, Heyn MP. FEBS Lett 581 5425-5429 (2007)
  41. Subpicosecond midinfrared spectroscopy of the Pfr reaction of phytochrome Agp1 from Agrobacterium tumefaciens. Schumann C, Gross R, Wolf MM, Diller R, Michael N, Lamparter T. Biophys J 94 3189-3197 (2008)
  42. FTIR study of the photoinduced processes of plant phytochrome phyA using isotope-labeled bilins and density functional theory calculations. Schwinté P, Foerstendorf H, Hussain Z, Gärtner W, Mroginski MA, Hildebrandt P, Siebert F. Biophys J 95 1256-1267 (2008)
  43. Photoconversion changes bilin chromophore conjugation and protein secondary structure in the violet/orange cyanobacteriochrome NpF2164g3' [corrected]. Lim S, Rockwell NC, Martin SS, Dallas JL, Lagarias JC, Ames JB. Photochem Photobiol Sci 13 951-962 (2014)
  44. Bacteriophytochrome Photoisomerization Proceeds Homogeneously Despite Heterogeneity in Ground State. Wang C, Flanagan ML, McGillicuddy RD, Zheng H, Ginzburg AR, Yang X, Moffat K, Engel GS. Biophys J 111 2125-2134 (2016)
  45. Apo-bacteriophytochromes modulate bacterial photosynthesis in response to low light. Fixen KR, Baker AW, Stojkovic EA, Beatty JT, Harwood CS. Proc Natl Acad Sci U S A 111 E237-44 (2014)
  46. Biliverdin amides reveal roles for propionate side chains in bilin reductase recognition and in holophytochrome assembly and photoconversion. Shang L, Rockwell NC, Martin SS, Lagarias JC. Biochemistry 49 6070-6082 (2010)
  47. Fluorescence of phytochrome adducts with synthetic locked chromophores. Zienicke B, Chen LY, Khawn H, Hammam MA, Kinoshita H, Reichert J, Ulrich AS, Inomata K, Lamparter T. J Biol Chem 286 1103-1113 (2011)
  48. Arabidopsis phytochrome a is modularly structured to integrate the multiple features that are required for a highly sensitized phytochrome. Oka Y, Ono Y, Toledo-Ortiz G, Kokaji K, Matsui M, Mochizuki N, Nagatani A. Plant Cell 24 2949-2962 (2012)
  49. High-resolution crystal structures of transient intermediates in the phytochrome photocycle. Carrillo M, Pandey S, Sanchez J, Noda M, Poudyal I, Aldama L, Malla TN, Claesson E, Wahlgren WY, Feliz D, Šrajer V, Maj M, Castillon L, Iwata S, Nango E, Tanaka R, Tanaka T, Fangjia L, Tono K, Owada S, Westenhoff S, Stojković EA, Schmidt M. Structure 29 743-754.e4 (2021)
  50. Solid-state NMR spectroscopic study of chromophore-protein interactions in the Pr ground state of plant phytochrome A. Song C, Essen LO, Gärtner W, Hughes J, Matysik J. Mol Plant 5 698-715 (2012)
  51. Ultrafast red light activation of Synechocystis phytochrome Cph1 triggers major structural change to form the Pfr signalling-competent state. Heyes DJ, Khara B, Sakuma M, Hardman SJ, O'Cualain R, Rigby SE, Scrutton NS. PLoS One 7 e52418 (2012)
  52. High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures. Sanchez JC, Carrillo M, Pandey S, Noda M, Aldama L, Feliz D, Claesson E, Wahlgren WY, Tracy G, Duong P, Nugent AC, Field A, Šrajer V, Kupitz C, Iwata S, Nango E, Tanaka R, Tanaka T, Fangjia L, Tono K, Owada S, Westenhoff S, Schmidt M, Stojković EA. Struct Dyn 6 054701 (2019)
  53. Steric Effects Govern the Photoactivation of Phytochromes. Falklöf O, Durbeej B. Chemphyschem 17 954-957 (2016)
  54. The photoreactions of recombinant phytochrome CphA from the cyanobacterium Calothrix PCC7601: a low-temperature UV-Vis and FTIR study. Schwinté P, Gärtner W, Sharda S, Mroginski MA, Hildebrandt P, Siebert F. Photochem Photobiol 85 239-249 (2009)
  55. Coordination of the biliverdin D-ring in bacteriophytochromes. Lenngren N, Edlund P, Takala H, Stucki-Buchli B, Rumfeldt J, Peshev I, Häkkänen H, Westenhoff S, Ihalainen JA. Phys Chem Chem Phys 20 18216-18225 (2018)
  56. On the origin of fluorescence in bacteriophytochrome infrared fluorescent proteins. Samma AA, Johnson CK, Song S, Alvarez S, Zimmer M. J Phys Chem B 114 15362-15369 (2010)
  57. X-ray radiation induces deprotonation of the bilin chromophore in crystalline D. radiodurans phytochrome. Li F, Burgie ES, Yu T, Héroux A, Schatz GC, Vierstra RD, Orville AM. J Am Chem Soc 137 2792-2795 (2015)
  58. A polarity probe for monitoring light-induced structural changes at the entrance of the chromophore pocket in a bacterial phytochrome. Borucki B, Lamparter T. J Biol Chem 284 26005-26016 (2009)
  59. Bacteriophytochrome controls carotenoid-independent response to photodynamic stress in a non-photosynthetic rhizobacterium, Azospirillum brasilense Sp7. Kumar S, Kateriya S, Singh VS, Tanwar M, Agarwal S, Singh H, Khurana JP, Amla DV, Tripathi AK. Sci Rep 2 872 (2012)
  60. Conformational heterogeneity of the Pfr chromophore in plant and cyanobacterial phytochromes. Velazquez Escobar F, von Stetten D, Günther-Lütkens M, Keidel A, Michael N, Lamparter T, Essen LO, Hughes J, Gärtner W, Yang Y, Heyne K, Mroginski MA, Hildebrandt P. Front Mol Biosci 2 37 (2015)
  61. Modeling of phytochrome absorption spectra. Falklöf O, Durbeej B. J Comput Chem 34 1363-1374 (2013)
  62. NMR spectroscopic investigation of mobility and hydrogen bonding of the chromophore in the binding pocket of phytochrome proteins. Röben M, Hahn J, Klein E, Lamparter T, Psakis G, Hughes J, Schmieder P. Chemphyschem 11 1248-1257 (2010)
  63. On the primary event of phytochrome: quantum chemical comparison of photoreactions at C4, C10 and C15. Durbeej B. Phys Chem Chem Phys 11 1354-1361 (2009)
  64. Which factors determine the acidity of the phytochromobilin chromophore of plant phytochrome? Anders Borg O, Durbeej B. Phys Chem Chem Phys 10 2528-2537 (2008)
  65. A non-covalently attached chromophore can mediate phytochrome B signaling in Arabidopsis. Oka Y, Kong SG, Matsushita T. Plant Cell Physiol 52 2088-2102 (2011)
  66. Fast Photochemistry of Prototypical Phytochromes-A Species vs. Subunit Specific Comparison. Ihalainen JA, Takala H, Lehtivuori H. Front Mol Biosci 2 75 (2015)
  67. Initial excited-state relaxation of the bilin chromophores of phytochromes: a computational study. Strambi A, Durbeej B. Photochem Photobiol Sci 10 569-579 (2011)
  68. Influence of the N-terminal segment and the PHY-tongue element on light-regulation in bacteriophytochromes. Gourinchas G, Vide U, Winkler A. J Biol Chem 294 4498-4510 (2019)
  69. Role of the protein cavity in phytochrome chromoprotein assembly and double-bond isomerization: a comparison with model compounds. Rohmer T, Lang C, Gärtner W, Hughes J, Matysik J. Photochem Photobiol 86 856-861 (2010)
  70. Structure of the response regulator RPA3017 involved in red-light signaling in Rhodopseudomonas palustris. Yang X, Zeng X, Moffat K, Yang X. Acta Crystallogr F Struct Biol Commun 71 1215-1222 (2015)
  71. Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy. Buhrke D, Michael N, Hamm P. Proc Natl Acad Sci U S A 119 e2206400119 (2022)
  72. Development of a multipurpose vacuum chamber for serial optical and diffraction experiments with free electron laser radiation. Rajkovic I, Hallmann J, Grübel S, More R, Quevedo W, Petri M, Techert S. Rev Sci Instrum 81 045105 (2010)
  73. MAS NMR on a Red/Far-Red Photochromic Cyanobacteriochrome All2699 from Nostoc. Xu QZ, Bielytskyi P, Otis J, Lang C, Hughes J, Zhao KH, Losi A, Gärtner W, Song C. Int J Mol Sci 20 E3656 (2019)
  74. Crystal structure of phytochromobilin synthase in complex with biliverdin IXα, a key enzyme in the biosynthesis of phytochrome. Sugishima M, Wada K, Fukuyama K, Yamamoto K. J Biol Chem 295 771-782 (2020)
  75. Light-induced complex formation of bacteriophytochrome RpBphP1 and gene repressor RpPpsR2 probed by SAXS. Papiz MZ, Bellini D, Evans K, Grossmann JG, Fordham-Skelton T. FEBS J 286 4261-4277 (2019)
  76. On the Role of the Conserved Histidine at the Chromophore Isomerization Site in Phytochromes. Kraskov A, Buhrke D, Scheerer P, Shaef I, Sanchez JC, Carrillo M, Noda M, Feliz D, Stojković EA, Hildebrandt P. J Phys Chem B 125 13696-13709 (2021)
  77. Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome. Hontani Y, Baloban M, Escobar FV, Jansen SA, Shcherbakova DM, Weißenborn J, Kloz M, Mroginski MA, Verkhusha VV, Kennis JTM. Commun Chem 4 3 (2021)
  78. Adaptive evolution in the GAF domain of phytochromes in gymnosperms. Wang J, Yan B, Chen G, Su Y, Wang T. Biochem Genet 48 236-247 (2010)
  79. Crystal structure and molecular mechanism of an E/F type bilin lyase-isomerase. Kumarapperuma I, Joseph KL, Wang C, Biju LM, Tom IP, Weaver KD, Grébert T, Partensky F, Schluchter WM, Yang X. Structure 30 564-574.e3 (2022)
  80. Kurt Schaffner: from organic photochemistry to photobiology. Gärtner W. Photochem Photobiol Sci 11 872-880 (2012)
  81. Pump-Probe Circular Dichroism Spectroscopy of Cyanobacteriochrome TePixJ Yields: Insights into Its Photoconversion. Clinger JA, Chen E, Kliger DS, Phillips GN. J Phys Chem B 125 202-210 (2021)
  82. Atomic force microscopy of red-light photoreceptors using peakforce quantitative nanomechanical property mapping. Kroeger ME, Sorenson BA, Thomas JS, Stojković EA, Tsonchev S, Nicholson KT. J Vis Exp e52164 (2014)
  83. Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering. Lee SJ, Kim TW, Kim JG, Yang C, Yun SR, Kim C, Ren Z, Kumarapperuma I, Kuk J, Moffat K, Yang X, Ihee H. Sci Adv 8 eabm6278 (2022)
  84. Mode of autophosphorylation in bacteriophytochromes RpBphP2 and RpBphP3. Kumarapperuma I, Tom IP, Bandara S, Montano S, Yang X. Photochem Photobiol Sci 22 1257-1266 (2023)
  85. Modulation of biliverdin dynamics and spectral properties by Sandercyanin. Ghosh S, Mondal S, Yadav K, Aggarwal S, Schaefer WF, Narayana C, Subramanian R. RSC Adv 12 20296-20304 (2022)
  86. Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome. Hontani Y, Baloban M, Escobar FV, Jansen SA, Shcherbakova DM, Weißenborn J, Kloz M, Mroginski MA, Verkhusha VV, Kennis JTM. Commun Chem 4 3 (2021)
  87. The phycoerythrobilin isomerization activity of MpeV in Synechococcus sp. WH8020 is prevented by the presence of a histidine at position 141 within its phycoerythrin-I β-subunit substrate. Carrigee LA, Frick JP, Liu X, Karty JA, Trinidad JC, Tom IP, Yang X, Dufour L, Partensky F, Schluchter WM. Front Microbiol 13 1011189 (2022)
  88. The structural effect between the output module and chromophore-binding domain is a two-way street via the hairpin extension. Kurttila M, Etzl S, Rumfeldt J, Takala H, Galler N, Winkler A, Ihalainen JA. Photochem Photobiol Sci 21 1881-1894 (2022)


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