PDBsum entry: 2k2n

Transferase

PDB id: 2k2n

Contents

Protein chain

172 a.a. *

Ligands

CYC

* Residue conservation analysis

PDB id:

2k2n

Name:

Transferase

Title:

Solution structure of a cyanobacterial phytochrome gaf domain in the red light-absorbing ground state

Structure:

Sensor protein. Chain: a. Fragment: gaf domain (unp residues 31-200). Synonym: syb-cph1(gaf). Engineered: yes

Source:

Synechococcus sp.. Organism_taxid: 316278. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

C.C.Cornilescu,G.Cornilescu,A.T.Ulijasz,R.D.Vierstra, J.L.Markley

Key ref:

G.Cornilescu et al. (2008). Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state. J Mol Biol, 383, 403-413. PubMed id: 18762196 DOI: 10.1016/j.jmb.2008.08.034

Date:

04-Apr-08 Release date: 23-Sep-08

Protein chain

Q2JIZ5  (Q2JIZ5_SYNJB) -  Sensor histidine kinase

Seq: 834 a.a.

Struc: 172 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Biological process: sensory perception (4 terms)
• Biochemical function: G-protein coupled photoreceptor activity (1 term)

DOI no: 10.1016/j.jmb.2008.08.034

J Mol Biol 383:403-413 (2008)

PubMed id: 18762196

Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state.

G.Cornilescu, A.T.Ulijasz, C.C.Cornilescu, J.L.Markley, R.D.Vierstra.

ABSTRACT

The unique photochromic absorption behavior of phytochromes (Phys) depends on numerous reversible interactions between the bilin chromophore and the associated polypeptide. To help define these dynamic interactions, we determined by NMR spectroscopy the first solution structure of the chromophore-binding cGMP phosphodiesterase/adenylcyclase/FhlA (GAF) domain from a cyanobacterial Phy assembled with phycocyanobilin (PCB). The three-dimensional NMR structure of Synechococcus OS-B' cyanobacterial Phy 1 in the red-light-absorbing state of Phy (Pr) revealed that PCB is bound to Cys138 of the GAF domain via the A-ring ethylidene side chain and is buried within the GAF domain in a ZZZsyn,syn,anti configuration. The D ring of the chromophore sits within a hydrophobic pocket and is tilted by approximately 80 degrees relative to the B/C rings by contacts with Lys52 and His169. The solution structure revealed remarkable flexibility for PCB and several adjacent amino acids, indicating that the Pr chromophore has more freedom in the binding pocket than anticipated. The propionic acid side chains of rings B and C and Arg101 and Arg133 nearby are especially mobile and can assume several distinct and energetically favorable conformations. Mutagenic studies on these arginines, which are conserved within the Phy superfamily, revealed that they have opposing roles, with Arg101 and Arg133 helping stabilize and destabilize the far-red-light-absorbing state of Phy (Pfr), respectively. Given the fact that the Synechococcus OS-B' GAF domain can, by itself, complete the Pr --> Pfr photocycle, it should now be possible to determine the solution structure of the Pfr chromophore and surrounding pocket using this Pr structure as a framework.

Selected figure(s)

Figure 1.
Fig. 1. Three-dimensional solution structure of the Pr state of the SyB-Cph1 GAF domain assembled with PCB. The highly dynamic first 30 amino acids and C-terminal 6His tag of the GAF domain of SyB-Cph1 are not modeled. PCB is shown in cyan, β strands are shown in blue, α helices are shown in red, and unstructured/loop regions are shown in yellow. (a) Superposition of the protein backbone from the 20 lowest-energy NMR conformers. (b) Superposition of the lowest-energy NMR structure for SyB-Cph1(GAF), with the high-resolution crystal structure of the GAF domain from DrBphP (PDB ID code 2O9B) assembled with BV (shown in gray). (c) Stereo view of the protein backbone of SyB-Cph1 in the lowest-energy NMR conformer (PDB ID code 2K2N). Specific α helices and β strands are labeled.

Figure 3.
Fig. 3. Mobility of Arg101 within the pocket adjacent to the B-ring propionic acid side chain (PA ring B) of PCB. (a) Overall view of the SyB-Cph1(GAF) domain highlighting Arg101 (magenta), Arg133 (yellow), and PA ring B (cyan). (b and c) Front and side closeup views of the 10 lowest-energy NMR conformers for Arg101 in its pocket. The positions of the Arg101 side chain in the 10 lowest-energy conformers are shown by van der Waals surfaces in (a) and by stick representations in (b) and (c).

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2008, 383, 403-413) copyright 2008.

Figures were selected by an automated process.