PDBsum entry 2o9c

Transferase

PDB id: 2o9c

Contents

Protein chain

319 a.a. *

Ligands

LBV

Waters ×318

* Residue conservation analysis

PDB id:

2o9c

Name:

Transferase

Title:

Crystal structure of bacteriophytochrome chromophore binding domain at 1.45 angstrom resolution

Structure:

Bacteriophytochrome. Chain: a. Fragment: chromophore binidng domain. Synonym: phytochrome-like protein. Engineered: yes. Mutation: yes

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Gene: bphp. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.45Å R-factor: 0.166 R-free: 0.192

Authors:

J.R.Wagner,J.S.Brunzelle,R.D.Vierstra,K.T.Forest

Key ref:

J.R.Wagner et al. (2007). High resolution structure of deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution. J Biol Chem, 282, 12298-12309. PubMed id: 17322301 DOI: 10.1074/jbc.M611824200

Date:

13-Dec-06 Release date: 06-Mar-07

Protein chain

Q9RZA4  (BPHY_DEIRA) -  Bacteriophytochrome from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 755 a.a.

Struc: 319 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.13.3 - histidine kinase.
• Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M611824200

J Biol Chem 282:12298-12309 (2007)

PubMed id: 17322301

High resolution structure of deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution.

J.R.Wagner, J.Zhang, J.S.Brunzelle, R.D.Vierstra, K.T.Forest.

ABSTRACT

Phytochromes are red/far red light photochromic photoreceptors that direct many photosensory behaviors in the bacterial, fungal, and plant kingdoms. They consist of an N-terminal domain that covalently binds a bilin chromophore and a C-terminal region that transmits the light signal, often through a histidine kinase relay. Using x-ray crystallography, we recently solved the first three-dimensional structure of a phytochrome, using the chromophore-binding domain of Deinococcus radiodurans bacterial phytochrome assembled with its chromophore, biliverdin IXalpha. Now, by engineering the crystallization interface, we have achieved a significantly higher resolution model. This 1.45A resolution structure helps identify an extensive buried surface between crystal symmetry mates that may promote dimerization in vivo. It also reveals that upon ligation of the C3(2) carbon of biliverdin to Cys(24), the chromophore A-ring assumes a chiral center at C2, thus becoming 2(R),3(E)-phytochromobilin, a chemistry more similar to that proposed for the attached chromophores of cyanobacterial and plant phytochromes than previously appreciated. The evolution of bacterial phytochromes to those found in cyanobacteria and higher plants must have involved greater fitness using more reduced bilins, such as phycocyanobilin, combined with a switch of the attachment site from a cysteine near the N terminus to one conserved within the cGMP phosphodiesterase/adenyl cyclase/FhlA domain. From analysis of site-directed mutants in the D. radiodurans phytochrome, we show that this bilin preference was partially driven by the change in binding site, which ultimately may have helped photosynthetic organisms optimize shade detection. Collectively, these three-dimensional structural results better clarify bilin/protein interactions and help explain how higher plant phytochromes evolved from prokaryotic progenitors.

Selected figure(s)

Figure 2.
FIGURE 2. DrCBD dimer interface. A, a shallow slab cut from a solvent-accessible surface of DrCBD reveals the interaction (same orientation as in Fig. 1C). B, the interface in the DrCBD-Y307S structure forms a more shape-complementary surface and buries 700 Å^2 additional surface area/dimer. Helices 4, 5, and 8 from the GAF domain are indicated.

Figure 4.
FIGURE 4. DrCBD-Y307S and its bilin-binding pocket. A, comparison of the bilin-binding pockets for the 1.45 Å resolution model of DrCBD-Y307S with the 2.5 Å resolution model of DrCBD (the latter shown in gray) (9). B, stereo view from above the bilin in the DrCBD-Y307S model. The dashed lines indicate interactions of the pyrrole water (water 12 (9)) with the BV nitrogen atoms, His^260 and the backbone O of Asp^207 as well as the 2.8-Å hydrogen bond between Tyr^263 and Asp^207. Two waters mediate the hydrogen-bonding network between His^290 and the C-ring propionate side chain. C, below the D-ring, a small cavity is apparent within the packed interior of the protein. Tyr^176 forms a hydrogen bond with water.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 12298-12309) copyright 2007.

Figures were selected by an automated process.