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Dimerization properties of the RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis.

Bellini D, Papiz MZ
Acta Crystallogr D Biol Crystallogr 68 1058-66 (2012)
Cited: 25 times
EuropePMC logo PMID: 22868772

Abstract

Bacteriophytochromes (BphPs) are biliverdin IXα-containing photoreceptors that photoconvert between red (Pr) and far-red (Pfr) absorbing states. BphPs are one half of a two-component system that transmits a light signal to a histidine kinase domain and then to a gene-response regulator. In Rhodopseudomonas palustris, synthesis of a light-harvesting complex (LH4) is controlled by two BphPs (RpBphP2 and RpBphP3). Despite their high sequence identity (52%), their absorption spectra are very different. The spectra of RpBphP2 exhibit classic Pr-to-Pfr photoconversion, whereas RpBphP3 quenches and a high-energy Pnr state emerges [Giraud et al. (2005), J. Biol. Chem. 280, 32389-32397]. Crystallization of the chromophore-binding domain (CBD) of RpBphP2 (RpBphP2-CBD) proved to be difficult and the structure of RpBphP3-CBD was used to crystallize RpBphP2-CBD* using homologue-directed mutagenesis. The structure shows that dimerization is an important factor in successful crystallization of RpBphP2-CBD* and arises from an N136R mutation. Mutations at this site correlate with an ability to dimerize in other truncated BphPs and may also be important for full-length dimer formation. Comparison of the RpBphP3-CBD and RpBphP2-CBD* biliverdin IXα pockets revealed that the former has additional hydrogen bonding around the B and D pyrrole rings that may constrain photoconversion to Pfr, resulting in a strained photoexcited Pnr state.

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  1. PAS domains in bacterial signal transduction. Stuffle EC, Johnson MS, Watts KJ. Curr Opin Microbiol 61 8-15 (2021)
  2. Phytochromes in Agrobacterium fabrum. Lamparter T, Xue P, Elkurdi A, Kaeser G, Sauthof L, Scheerer P, Krauß N. Front Plant Sci 12 642801 (2021)

Articles - 4e04 mentioned but not cited (9)

  1. Allosteric effects of chromophore interaction with dimeric near-infrared fluorescent proteins engineered from bacterial phytochromes. Stepanenko OV, Baloban M, Bublikov GS, Shcherbakova DM, Stepanenko OV, Turoverov KK, Kuznetsova IM, Verkhusha VV. Sci Rep 6 18750 (2016)
  2. Ultrafast excited-state dynamics and fluorescence deactivation of near-infrared fluorescent proteins engineered from bacteriophytochromes. Zhu J, Shcherbakova DM, Hontani Y, Verkhusha VV, Kennis JT. Sci Rep 5 12840 (2015)
  3. Proteins analysed as virtual knots. Alexander K, Taylor AJ, Dennis MR. Sci Rep 7 42300 (2017)
  4. Interaction of Biliverdin Chromophore with Near-Infrared Fluorescent Protein BphP1-FP Engineered from Bacterial Phytochrome. Stepanenko OV, Stepanenko OV, Kuznetsova IM, Shcherbakova DM, Verkhusha VV, Turoverov KK. Int J Mol Sci 18 (2017)
  5. Optimized Longitudinal Monitoring of Stem Cell Grafts in Mouse Brain Using a Novel Bioluminescent/Near Infrared Fluorescent Fusion Reporter. Mezzanotte L, Iljas JD, Que I, Chan A, Kaijzel E, Hoeben R, Löwik C. Cell Transplant 26 1878-1889 (2017)
  6. Impact of Double Covalent Binding of BV in NIR FPs on Their Spectral and Physicochemical Properties. Stepanenko OV, Kuznetsova IM, Turoverov KK, Stepanenko OV. Int J Mol Sci 23 7347 (2022)
  7. Near-Infrared Markers based on Bacterial Phytochromes with Phycocyanobilin as a Chromophore. Stepanenko OV, Stepanenko OV, Shpironok OG, Fonin AV, Kuznetsova IM, Turoverov KK. Int J Mol Sci 20 (2019)
  8. 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)
  9. mRhubarb: Engineering of monomeric, red-shifted, and brighter variants of iRFP using structure-guided multi-site mutagenesis. Rogers OC, Johnson DM, Firnberg E. Sci Rep 9 15653 (2019)


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  2. Light-induced Changes in the Dimerization Interface of Bacteriophytochromes. Takala H, Björling A, Linna M, Westenhoff S, Ihalainen JA. J. Biol. Chem. 290 16383-16392 (2015)
  3. 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)
  4. Light Signaling Mechanism of Two Tandem Bacteriophytochromes. Yang X, Stojković EA, Ozarowski WB, Kuk J, Davydova E, Moffat K. Structure 23 1179-1189 (2015)
  5. Novel near-infrared BiFC systems from a bacterial phytochrome for imaging protein interactions and drug evaluation under physiological conditions. Chen M, Li W, Zhang Z, Liu S, Zhang X, Zhang XE, Cui Z. Biomaterials 48 97-107 (2015)
  6. A knot in the protein structure - probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochrome. Stepanenko OV, Bublikov GS, Stepanenko OV, Shcherbakova DM, Verkhusha VV, Turoverov KK, Kuznetsova IM. FEBS J. 281 2284-2298 (2014)
  7. 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)
  8. Direct multiplex imaging and optogenetics of Rho GTPases enabled by near-infrared FRET. Shcherbakova DM, Cox Cammer N, Huisman TM, Verkhusha VV, Hodgson L. Nat. Chem. Biol. 14 591-600 (2018)
  9. 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)
  10. 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)
  11. Near infrared fluorescent biliproteins generated from bacteriophytochrome AphB of Nostoc sp. PCC 7120. Yuan C, Li HZ, Tang K, Gärtner W, Scheer H, Zhou M, Zhao KH. Photochem. Photobiol. Sci. 15 546-553 (2016)
  12. The role of local and remote amino acid substitutions for optimizing fluorescence in bacteriophytochromes: A case study on iRFP. Buhrke D, Velazquez Escobar F, Sauthof L, Wilkening S, Herder N, Tavraz NN, Willoweit M, Keidel A, Utesch T, Mroginski MA, Schmitt FJ, Hildebrandt P, Friedrich T. Sci Rep 6 28444 (2016)
  13. 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)
  14. 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)


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