PDBsum entry: 2ool

Signaling protein

PDB-id: 2ool

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

304 a.a. *

Ligands

LBV ×2

Waters ×215

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

2ool

Name:

Signaling protein

Title:

Crystal structure of the chromophore-binding domain of an unusual bacteriophytochrome rpbphp3 from r. Palustris

Structure:

Sensor protein. Chain: a, b. Fragment: chormophore binding domain (residues: 1-337). Engineered: yes

Source:

Rhodopseudomonas palustris cga009. Organism_taxid: 258594. Strain: cga009. Gene: phyb2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

UniProt:

Chains A, B: Q6N5G2 (Q6N5G2_RHOPA)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

775 a.a.

Struc:

304 a.a.

Key:

PfamA domain

Secondary structure

Enzyme class:

E.C.2.7.13.3   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP + protein L-histidine = ADP + protein N-phospho-L-histidine

Resolution:

2.20Å

R-factor:

0.192

R-free:

0.231

Authors:

X.Yang,E.A.Stojkovic,J.Kuk,K.Moffat

Key ref:

X.Yang et al. (2007). Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion.. Proc Natl Acad Sci U S A, 104, 12571-12576. [PubMed id: 17640891] [DOI: 10.1073/pnas.0701737104]

Date:

25-Jan-07

Release date:

10-Jul-07

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1073/pnas.0701737104

Proc Natl Acad Sci U S A 104:12571-12576 (2007)

PubMed id: 17640891

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

X.Yang, E.A.Stojkovic, J.Kuk, K.Moffat.

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.

Selected figure(s)

Figure 1.
Fig. 1. Crystal structure of RpBphP3-CBD. (a) Domain structure of the full-length Bph RpBphP3. (b) Ribbon diagram of the two RpBphP3-CBD molecules in the asymmetric unit. The PAS domain is in yellow, and the GAF domain is in green. (c) Superposition of the crystal structures of RpBphP3-CBD (PDB ID code 2OOL, in yellow and green) and DrBphP-CBD (PDB ID code 2O9C, in light blue). (d) The F[o] – F[c] omit map in the region of chromophore. The chromophore is shown as 2(S),3(E)-P B covalently linked to Cys-28.

Figure 4.
Fig. 4. VDW surface of the RpBphP3-CBD structure. Residues Tyr-272, Asp-216, and Leu-207-Phe-210-Phe-212 in the 15Ea pocket (colored in maroon) form a continuous surface patch and shield ring D of the chromophore (in cyan) in the GAF domain.

Figures were selected by an automated process.