PDBsum entry: 3c2w

Signaling protein

PDB id: 3c2w

Contents

Protein chains

(+ 2 more) 478 a.a. *

Ligands

BLA ×8

Waters ×30

* Residue conservation analysis

PDB id:

3c2w

Name:

Signaling protein

Title:

Crystal structure of the photosensory core domain of p. Aeruginosa bacteriophytochrome pabphp in the pfr state

Structure:

Bacteriophytochrome. Chain: a, b, c, d, e, f, g, h. Fragment: photosensory core domain. Synonym: phytochrome-like protein. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Strain: pa01. Gene: bphp, pa4117. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.90Å R-factor: 0.222 R-free: 0.283

Authors:

X.Yang,J.Kuk,K.Moffat

Key ref:

X.Yang et al. (2008). Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction. Proc Natl Acad Sci U S A, 105, 14715-14720. PubMed id: 18799746 DOI: 10.1073/pnas.0806718105

Date:

25-Jan-08 Release date: 23-Sep-08

Protein chains

Q9HWR3  (BPHY_PSEAE) -  Bacteriophytochrome

Seq: 728 a.a.

Struc: 478 a.a.

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: sensory perception (4 terms)
• Biochemical function: receptor activity (2 terms)

reference

DOI no: 10.1073/pnas.0806718105

Proc Natl Acad Sci U S A 105:14715-14720 (2008)

PubMed id: 18799746

Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction.

X.Yang, J.Kuk, K.Moffat.

ABSTRACT

Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 A resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an "arm" structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.

Selected figure(s)

Figure 1.
Crystal structure of wild-type PaBphP-PCD. (A) Ribbon diagram of the dimeric PaBphP-PCD structure. The PAS, GAF, and PHY domains of one monomer are highlighted in yellow, green, and blue, respectively. Helices in the GAF and PHY domains are identified by letters (A–E). (B) The PAS, GAF, and PHY domains are integrated via extensive interdomain interactions and converge on the chromophore binding site (cyan). (C) Accessory structure elements (gray) decorate the common cores of the PAS, GAF, and PHY domains and are spatially clustered near the chromophore (cyan) and as helical bundles at the dimer interface. (D) The core of the PAS, GAF, and PHY domains contains an antiparallel β sheet with strands in the spatial order of 2–1–5–4–3 and a variable connector between strands 2 and 3 that contains helix C. (E) Both core and accessory elements are highlighted in a topologic diagram of the PaBphP-PCD structure.

Figure 4.
A domain architecture model of the full-length dimeric PaBphP based on the PaBphP-PCD dimer structure and the sensor HK structure (PDB accession ID 2C2A) (PAS, GAF, and PHY in green; HK in blue; BV in cyan).

Figures were selected by the author.