PDBsum entry: 1kou

Photosynthesis

PDB id: 1kou

Contents

Protein chain

120 a.a. *

Ligands

DHC

NBU

Waters ×135

* Residue conservation analysis

PDB id:

1kou

Name:

Photosynthesis

Title:

Crystal structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 a resolution

Structure:

Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes

Source:

Halorhodospira halophila. Organism_taxid: 1053. Gene: pyp. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.16Å R-factor: 0.162 R-free: 0.203

Authors:

D.M.F.Van Aalten,W.Crielaard,K.J.Hellingwerf,L.Joshua-Tor

Key ref:

D.M.van Aalten et al. (2002). Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 A resolution. Acta Crystallogr D Biol Crystallogr, 58, 585-590. PubMed id: 11914481 DOI: 10.1107/S0907444902001257

Date:

22-Dec-01 Release date: 03-Apr-02

Protein chain

P16113  (PYP_HALHA) -  Photoactive yellow protein

Seq: 125 a.a.

Struc: 120 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: response to stimulus (5 terms)
• Biochemical function: signal transducer activity (3 terms)

DOI no: 10.1107/S0907444902001257

Acta Crystallogr D Biol Crystallogr 58:585-590 (2002)

PubMed id: 11914481

Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 A resolution.

D.M.van Aalten, W.Crielaard, K.J.Hellingwerf, L.Joshua-Tor.

ABSTRACT

A structural study is described of the photoactive yellow protein (PYP) reconstituted with the chromophore derivative 3,4-dihydroxycinnamic acid. The crystal structure of PYP reconstituted with this chromophore at 1.16 A resolution is reported in space group P6(5). This is the first high-resolution structure of a photoreceptor containing a modified chromophore. The introduction of an extra hydroxyl group in the native chromophore (i.e. p-coumaric acid) appears to perturb the structure of the hybrid yellow protein only slightly. The chromophore is bound by the protein in two different conformations, separated by a rotation of 180 degrees of the catechol ring. In combination with available spectroscopic data, it is concluded that the caffeic acid chromophore binds to the protein in a strained conformation, which leads to a faster ejection from the chromophore-binding pocket upon pB formation.

Selected figure(s)

Figure 2.
Figure 2 Stereoviews of the electron density around the chromophore. F[o] - F[c] maps just before including the chromophore are shown in magenta. 2F[o] - F[c] maps after building in the chromophore and subsequent refinement are show in cyan. (a) CAFPYP (15-1.39 Å CNS maps), (b) CAFPYP (15-1.16 Å SHELX maps). levels were 1.0 and 2.5 for the 2F[o] - F[c] and F[o] - F[c] CNS maps, respectively, in (a) and 1.75 and 2.75 for the 2F[o] - F[c] and F[o] - F[c] SHELX maps, respectively, in (b). In (b) the two alternate conformations of the chromophore are colored yellow and green. See text for details.

Figure 4.
Figure 4 Electrostatic interactions in the chromophore-binding pocket. WTPYP is shown in (a) and the two alternate conformations of the caffeic acid chromophore in CAFPYP are shown in (b) (occupancy 0.67) and (c) (occupancy 0.33). A molecular surface was calculated with GRASP (Nicholls et al., 1991[Nicholls, A., Sharp, K. & Honig, B. (1991). Proteins, 11, 281-296.]) and colored by electrostatic potential. For WTPYP, the phenolic chromophore O atom was assigned a charge of -0.5 and the Glu46 O atoms charges of -0.25. For CAFPYP, charges were -0.25 for the Glu46 and chromophore ring O atoms.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 585-590) copyright 2002.

Figures were selected by an automated process.