PDBsum entry 2dre

Plant protein

PDB id: 2dre

Contents

Protein chains

172 a.a. *

173 a.a. *

Ligands

CLA ×4

Waters ×555

* Residue conservation analysis

PDB id:

2dre

Name:

Plant protein

Title:

Crystal structure of water-soluble chlorophyll protein from lepidium virginicum at 2.00 angstrom resolution

Structure:

Water-soluble chlorophyll protein. Chain: a, b, c, d. Fragment: residues 1-180

Source:

Lepidium virginicum. Organism_taxid: 59292. Tissue: leaf

Resolution:

2.00Å R-factor: 0.243 R-free: 0.280

Authors:

D.Horigome,H.Satoh,N.Itoh,K.Mitsunaga,I.Oonishi,A.Nakagawa,A.Uchida

Key ref:

D.Horigome et al. (2007). Structural mechanism and photoprotective function of water-soluble chlorophyll-binding protein. J Biol Chem, 282, 6525-6531. PubMed id: 17170107 DOI: 10.1074/jbc.M609458200

Date:

08-Jun-06 Release date: 26-Dec-06

Protein chain

O04797  (O04797_LEPVR) -  Water-soluble chlorophyll protein from Lepidium virginicum

Seq: 223 a.a.

Struc: 172 a.a.

Protein chains

O04797  (O04797_LEPVR) -  Water-soluble chlorophyll protein from Lepidium virginicum

Seq: 223 a.a.

Struc: 173 a.a.

DOI no: 10.1074/jbc.M609458200

J Biol Chem 282:6525-6531 (2007)

PubMed id: 17170107

Structural mechanism and photoprotective function of water-soluble chlorophyll-binding protein.

D.Horigome, H.Satoh, N.Itoh, K.Mitsunaga, I.Oonishi, A.Nakagawa, A.Uchida.

ABSTRACT

A water-soluble chlorophyll-binding protein (WSCP) is the single known instance of a putative chlorophyll (Chl) carrier in green plants. Recently the photoprotective function of WSCP has been demonstrated by EPR measurements; the light-induced singlet-oxygen formation of Chl in the WSCP tetramer is about four times lower than that of unbound Chl. This paper describes the crystal structure of the WSCP-Chl complex purified from leaves of Lepidium virginicum (Virginia pepperweed) to clarify the mechanism of its photoprotective function. The WSCP-Chl complex is a homotetramer comprising four protein chains of 180 amino acids and four Chl molecules. At the center of the complex one hydrophobic cavity is formed in which all of the four Chl molecules are tightly packed and isolated from bulk solvent. With reference to the novel Chl-binding mode, we propose that the photoprotection mechanism may be based on the inhibition of physical contact between the Chl molecules and molecular oxygen.

Selected figure(s)

Figure 1.
FIGURE 1. Overall structure of the tetrameric WSCP-Chl complex and Chl-binding cavity. a, the overall structure is shown in a ribbon model of the protein moiety (WSCP) and in a Corey-Pauling-Koltun model of Chl molecules. The four monomers are shown in yellow, green, blue, and red. The principal dimers are the pairs of chains A and B and chains C and D. b, chain D of the tetrameric WSCP-Chl complex (ribbon model) and Chl-4 (stick model) are shown with the same orientation as in a. c, the hydrophobic cavity enclosing the four Chl molecules is shown as a blue transparent surface. The residues of 31–61, 86–96, and 152–156 of each WSCP monomer are shown. d, a cut-away view of the surface of the cavity shown in dark blue (outside) and silver (inside). The four Chl molecules are shown in a stick model with the same color coding as in a. Molecular graphics were generated with the program Chimera (41).

Figure 2.
FIGURE 2. Stoichiometric binding between the WSCP monomer and Chl. Chains A and B of the WSCP tetramer and Chl-1 are shown in ribbon models and a stick model, respectively, with the same color coding as in Fig. 1. The [A]-weighted 2F[o] - F[c] electron density map (4.0 contour) for the central Mg^2+ ion is shown in pink mesh. The water molecule in the Chl-binding cavity forms two hydrogen bonds (pink lines). Chl-2 is omitted for clarity.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 6525-6531) copyright 2007.

Figures were selected by an automated process.