PDBsum entry: 2vea

Transferase

PDB id: 2vea

Contents

Protein chain

500 a.a. *

Ligands

CYC

Waters ×29

* Residue conservation analysis

PDB id:

2vea

Name:

Transferase

Title:

The complete sensory module of the cyanobacterial phytochrome cph1 in the pr-state.

Structure:

Phytochrome-like protein cph1. Chain: a. Fragment: sensory module, residues 1-514. Synonym: light-regulated histidine kinase 1, bacteriophytochrome cph1, cyanobacterial phytochrome cph1. Engineered: yes. Other_details: thioether linkage between c259 and c3(1) atom of phycocyanobilin chromophore

Source:

Synechocystis sp. Pcc 6803. Organism_taxid: 1148. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: p45.2.

Resolution:

2.21Å R-factor: 0.245 R-free: 0.271

Authors:

L.-O.Essen,J.Mailliet,J.Hughes

Key ref:

L.O.Essen et al. (2008). The structure of a complete phytochrome sensory module in the Pr ground state. Proc Natl Acad Sci U S A, 105, 14709-14714. PubMed id: 18799745 DOI: 10.1073/pnas.0806477105

Date:

18-Oct-07 Release date: 30-Sep-08

Protein chain

Q55168  (PHY1_SYNY3) -  Phytochrome-like protein cph1

Seq: 748 a.a.

Struc: 500 a.a.*

* PDB and UniProt seqs differ at 6 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

 Gene Ontology (GO) functional annotation 

• Biological process: signal transduction (5 terms)
• Biochemical function: signal transducer activity (3 terms)

reference

DOI no: 10.1073/pnas.0806477105

Proc Natl Acad Sci U S A 105:14709-14714 (2008)

PubMed id: 18799745

The structure of a complete phytochrome sensory module in the Pr ground state.

L.O.Essen, J.Mailliet, J.Hughes.

ABSTRACT

Phytochromes are red/far-red photochromic biliprotein photoreceptors, which in plants regulate seed germination, stem extension, flowering time, and many other light effects. However, the structure/functional basis of the phytochrome photoswitch is still unclear. Here, we report the ground state structure of the complete sensory module of Cph1 phytochrome from the cyanobacterium Synechocystis 6803. Although the phycocyanobilin (PCB) chromophore is attached to Cys-259 as expected, paralleling the situation in plant phytochromes but contrasting to that in bacteriophytochromes, the ZZZssa conformation does not correspond to that expected from Raman spectroscopy. We show that the PHY domain, previously considered unique to phytochromes, is structurally a member of the GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) family. Indeed, the tandem-GAF dumbbell revealed for phytochrome sensory modules is remarkably similar to the regulatory domains of cyclic nucleotide (cNMP) phosphodiesterases and adenylyl cyclases. A unique feature of the phytochrome structure is a long, tongue-like protrusion from the PHY domain that seals the chromophore pocket and stabilizes the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue. The structure that we present provides a framework for light-driven signal transmission in phytochromes.

Selected figure(s)

Figure 1.
Structure and spectral characteristics of the Cph1 phytochrome sensory module from Synechocystis 6803. (A) Domain boundaries of Cph1 phytochrome. In the recombinant Cph1 sensory module described, the C-terminal histidine kinase transmitter (Leu-515–Asn-748) is replaced by a (His)[6] tag. (B) Ribbon representation of the sensory module structure showing the N-terminal α-helix (green) and PAS (blue), GAF (orange) and PHY (red) domains. The PCB chromophore (cyan) is covalently attached to Cys-259. Disordered loop regions (Gln-73–Arg-80, Gly-100–Asp-101, Arg-148–Gln-150, and Glu-463–Gly-465) are indicated as dotted lines. The molecular surface calculated by PYMOL (probe radius, 1.4 Å) is shown in gray. (C) Omit electron density of the adduct between the PCB chromophore and Cys-259 contoured at 2σ. (D) UV/Vis spectra of the Cph1 sensory module in solution at room temperature (red line) and in crystalline form at 100 K (■) in the Pr state (Upper) and after red light irradiation (Lower). Whereas in solution a photoequilibrium at 70% Pfr is reached, the mole fraction is ≈50% in the crystal. Spectra from crystals were recorded at the Cryobench of the ESRF, Grenoble. Photoconversion was done by irradiating for 10 s at room temperature with a 635 nm argon laser focused to 100 μm.

Figure 3.
The tongue and the chromophore binding pocket. (A) Space-filling model of Cph1 (Left) in comparison with known bacteriophytochrome structures (12, 13). The PCB chromophore (cyan) is completely sealed from solvent access by the tongue (dark red) in contrast to the exposed biliverdin (green) in the incomplete bidomains. (B and C) The tripartite PCB-binding pocket of Cph1 comprising the GAF-domain (orange), the tongue-like protrusion from the PHY domain (red) and the N-terminal α[1]-helix (green). Waters are shown as red spheres. (B) Edge-on view of the pocket highlighting the collinear arrangement of the N-terminal α[1]-helix and α[7]-helix of the GAF domain and their interaction with the chromophore and the tongue. (C) The conformation of the PCB chromophore (cyan) within the PCB-binding site adopts a ZZZssa configuration similar to that of BV in bacteriophytochromes (12, 13). For clarity, α[8]-helix of the GAF domain as well as Tyr-263 and Phe-475 have been omitted.

Figures were selected by the author.