Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 38, 2008, Pages 14715-14720

  Yang, Xiaojing ^a   Kuk, Jane ^a   Moffat, Keith ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

Photoreceptor; Phytochrome

Indexed keywords

ADENYLATE CYCLASE; BACTERIOPHYTOCHRMOE; PHYTOCHROME; PROTEIN HISTIDINE KINASE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PSEUDOMONAS AERUGINOSA; SIGNAL TRANSDUCTION;

BACTERIAL PROTEINS; MODELS, MOLECULAR; PHOTOCHEMISTRY; PHYTOCHROME; PROTEIN STRUCTURE, TERTIARY; PSEUDOMONAS AERUGINOSA; SIGNAL TRANSDUCTION;

FUNGI; PSEUDOMONAS AERUGINOSA;

EID: 55749108880     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0806718105     Document Type: Article

References (44)

1. Rockwell NC, Su YS, Lagarias JC (2006) Phytochrome structure and signaling mechanisms. Annu Rev Plant Biol 57:837-858.
2. Rockwell NC, Lagarias JC (2006) The structure of phytochrome: A picture is worth a thousand spectra. Plant Cell 18:4-14.
3. Wagner JR, Zhang J, Brunzelle JS, Vierstra RD, Forest KT (2007) High resolution structure of Deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution. J Biol Chem 282:12298-12309.
4. Wagner JR, Brunzelle JS, Forest KT, Vierstra RD (2005) A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 438:325-331.
5. Yang X, Stojkovic EA, Kuk J, Moffat K (2007) Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion. Proc Natl Acad Sci USA 104:12571-12576.
6. Park CM, Bhoo SH, Song PS (2000) Inter-domain crosstalk in the phytochrome molecules. Semin Cell Dev Biol 11:449-456.
7. Wu SH, Lagarias JC (2000) Defining the bilin lyase domain: Lessons from the extended phytochrome superfamily. Biochemistry 39:13487-13495.
8. Fischer AJ, Lagarias JC (2004) Harnessing phytochrome's glowing potential. Proc Natl Acad Sci USA 101:17334-17339.
9. Oka Y, et al. (2004) Functional analysis of a 450-amino acid N-terminal fragment of phytochrome B in Arabidopsis. Plant Cell 16:2104-2116.
10. van Thor JJ, Ronayne KL, Towrie M (2007) Formation of the early photoproduct lumi-R of cyanobacterial phytochrome cph1 observed by ultrafast mid-infrared spectroscopy. J Am Chem Soc 129:126-132.
11. Schumann C, Gross R, Michael N, Lamparter T, Diller R (2007) Sub-picosecond mid-infrared spectroscopy of phytochrome Agp1 from Agrobacterium tumefaciens. Chemphyschem 8:1657-1663.
12. Mroginski MA, Murgida DH, Hildebrandt P (2007) The chromophore structural changes during the photocycle of phytochrome: A combined resonance Raman and quantum chemical approach. Acc Chem Res 40:258-266.
13. van Thor JJ, Mackeen M, Kuprov I, Dwek RA, Wormald MR (2006) Chromophore structure in the photocycle of the cyanobacterial phytochrome Cph1. Biophys J 91:1811-1822.
14. Inomata K, et al. (2006) Assembly of synthetic locked chromophores with agrobacterium phytochromes Agp1 and Agp2. J Biol Chem 281:28162-28173.
15. Borucki B, et al. (2005) Light-induced proton release of phytochrome is coupled to the transient deprotonation of the tetrapyrrole chromophore. J Biol Chem 280:34358-34364.
16. Inomata K, et al. (2005) Sterically locked synthetic bilin derivatives and phytochrome Agp1 from Agrobacterium tumefaciens form photoinsensitive Pr- and Pfr-like adducts. J Biol Chem 280:24491-24497.
17. Montgomery BL, Lagarias JC (2002) Phytochrome ancestry: Sensors of bilins and light. Trends Plants Sci 7:357-366.
18. Ponting CP, Aravind L (1997) PAS: A multifunctional domain family comes to light. Curr Biol 7:R674-R677.
19. Aravind L, Ponting CP (1997) The GAF domain: An evolutionary link between diverse phototransducing proteins. Trends Biochem Sci 22:458-459.
20. Wagner JR, et al. (2008) Mutational analysis of Deinococcus radiodurans bacteriophytochrome reveals key amino acids necessary for the photochromicity and proton exchange cycle of phytochromes. J Biol Chem 283:12212-12226.
21. Giraud E, et al. (2005) A new type of bacteriophytochrome acts in tandem with a classical bacteriophytochrome to control the antennae synthesis in Rhodopseudomonas palustris. J Biol Chem 280:32389-32397.
22. Tasler R, Moises T, Frankenberg-Dinkel N (2005) Biochemical and spectroscopic characterization of the bacterial phytochrome of Pseudomonas aeruginosa. FEBS J 272:1927-1936.
23. Karniol B, Vierstra RD (2003) The pair of bacteriophytochromes from Agrobacterium tumefaciens are histidine kinases with opposing photobiological properties. Proc Natl Acad Sci USA 100:2807-2812.
24. Lamparter T, Michael N, Mittmann F, Esteban B (2002) Phytochrome from Agrobacterium tumefaciens has unusual spectral properties and reveals an N-terminal chromophore attachment site. Proc Natl Acad Sci USA 99:11628-11633.
25. Giraud E, et al. (2002) Bacteriophytochrome controls photosystem synthesis in anoxygenic bacteria. Nature 417:202-205.
26. Schmidt M, Patel A, Zhao Y, Reuter W (2007) Structural basis for the photochemistry of alpha-phycoerythrocyanin. Biochemistry 46:416-423.
27. Fischer AJ, et al. (2005) Multiple roles of a conserved GAF domain tyrosine residue in cyanobacterial and plant phytochromes. Biochemistry 44:15203-15215.
28. Anantharaman V, Balaji S, Aravind L (2006) The signaling helix: A common functional theme in diverse signaling proteins. Biol Direct 1:25.
29. Strickland D, Moffat K, Sosnick T (2008) Light-activated DNA binding in a designed allosteric protein. Proc Natl Acad Sci USA 105:10709-10714.
30. Marina A, Waldburger CD, Hendrickson WA (2005) Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein. EMBO J 24:4247-4259.
31. Marina A, Mott C, Auyzenberg A, Hendrickson WA, Waldburger CD (2001) Structural and mutational analysis of the PhoQ histidine kinase catalytic domain. Insight into the reaction mechanism. J Biol Chem 276:41182-41190.
32. Yang Y, Inouye M (1991) Intermolecular complementation between two defective mutant signal transducing receptors of Escherichia coli. Proc Natl Acad Sci USA 88:11057-11061.
33. Swanson RV, Bourret RB, Simon MI (1993) Intermolecular complementation of the kinase activity of CheA. Mol Microbiol 8:435-441.
34. Svergun DI, Barberato C, Koch MHJ (1995) CRYSOL - A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Mol Biol 112:535-542.
35. Evans K, Grossmann JG, Fordham-Skelton AP, Papiz MZ (2006) Small-angle x-ray scattering reveals the solution structure of a bacteriophytochrome in the catalytically active Pr state. J Mol Biol 364:655-666.
36. Doublie S (1997) Preparation of selenomethionyl proteins for phase determination. Methods Enzymol 276:523-530.
37. Otwinowski Z, Minor W (1997) Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol 276(part A):307-326.
38. Terwilliger JD (2000) A likelihood-based extended admixture model of oligogenic inheritance in 'model-based' and 'model-free' analysis. Eur J Hum Genet 8:399-406.
39. La Fortelle Ed, Bricogne G (1997) Maximum-likelihood heavy-atom parameter refinement for the multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol 276:472-494.
40. Brunger AT, Adams PD, Clore M, Delano WL (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D(54):905-921.
41. Vagin AA, et al. (2004) REFMAC5 dictionary: Organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr D(60):2184-2195.
42. Adams PD, et al. (2002) PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58(part 11):1948-1954.
43. Read RJ (2001) Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr D(57):1373-1382.
44. Emsley P CK (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D(60):2126-2132.