PDBsum entry 2ibz

Oxidoreductase

PDB id: 2ibz

Contents

Protein chains

431 a.a.

352 a.a.

385 a.a.

245 a.a.

185 a.a.

74 a.a.

125 a.a.

93 a.a.

55 a.a.

127 a.a.

107 a.a.

Ligands

HEC ×3

UQ6

SMA

FES

Waters ×340

References listed in PDB file

Key reference

Title

A comparison of stigmatellin conformations, Free and bound to the photosynthetic reaction center and the cytochrome bc1 complex.

Authors

C.R.Lancaster, C.Hunte, J.Kelley, B.L.Trumpower, R.Ditchfield.

Ref.

J Mol Biol, 2007, 368, 197-208. [DOI no: 10.1016/j.jmb.2007.02.013]

PubMed id

17337272

Abstract

We describe in detail the conformations of the inhibitor stigmatellin in its free form and bound to the ubiquinone-reducing (Q(B)) site of the reaction center and to the ubiquinol-oxidizing (Q(o)) site of the cytochrome bc(1) complex. We present here the first structures of a stereochemically correct stigmatellin in complexes with a bacterial reaction center and the yeast cytochrome bc1 complex. The conformations of the inhibitor bound to the two enzymes are not the same. We focus on the orientations of the stigmatellin side-chain relative to the chromone head group, and on the interaction of the stigmatellin side-chain with these membrane protein complexes. The different conformations of stigmatellin found illustrate the structural variability of the Q sites, which are affected by the same inhibitor. The free rotation about the chi1 dihedral angle is an essential factor for allowing stigmatellin to bind in both the reaction center and the cytochrome bc1 pocket.

Figure 5.
Figure 5. A comparison of non-bonding interactions at the stigmatellin-binding sites of (a) the Rp. viridis RC and (b) the S. cerevisiae cytochrome bc[1] complex. For clarity, interactions involving the chromone head group other than hydrogen bonding interactions (shown in light blue)^13.^ and ^14. are omitted. Labelled cyt bc[1] complex residues are from cytochrome b with the exception of the Rieske protein residue His181*. Interatomic distances of equal to or less than 4.0 Å involving the first half of the stigmatellin tail are indicated in red, those with the second, terminal half, in green. For clarity, in cases of multiple interactions fulfilling the distance criterion for the same stigmatellin atom, only the shortest distances are shown.

Figure 6.
Figure 6. Preference in the RC Q[B] site for the distorted stigmatellin conformer (Stereo view). RC residues that prevent the binding of stigmatellin in the theoretical lowest energy type 1 conformation (light blue) and in the cyt bc[1]-bound type 2 conformation (pink). Otherwise, color-coding and labeling are the same as in Figure 4.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 368, 197-208) copyright 2007.