4E04

RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis.

Summary for 4E04

• Entry DOI: 10.2210/pdb4e04/pdb
• Related: 2OOL
• Descriptor: Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1, 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid (3 entities in total)
• Functional Keywords: bacteriophytochrome chromophore binding domain, two component regulator, response regulator rpa3017, phosphorylation, phosphotransfer, transferase, signaling protein
• Biological source: Rhodopseudomonas palustris
• Total number of polymer chains: 2
• Total formula weight: 73545.57

Authors

Bellini, D.,Papiz, M.Z. (deposition date: 2012-03-02, release date: 2012-07-25, Last modification date: 2024-11-27)

Primary citation

Bellini, D.,Papiz, M.Z.
Dimerization properties of the RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis.
Acta Crystallogr.,Sect.D, 68:1058-1066, 2012

PubMed 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.

PubMed: 22868772
DOI: 10.1107/S0907444912020537

Experimental method

X-RAY DIFFRACTION (1.79 Å)