PDBsum entry 2dge

Electron transport

PDB id: 2dge

Contents

Protein chains

102 a.a. *

Ligands

HEM ×4

Metals

_ZN ×2

Waters ×248

* Residue conservation analysis

PDB id:

2dge

Name:

Electron transport

Title:

Crystal structure of oxidized cytochrome c6a from arabidopsis thaliana

Structure:

Cytochrome c6. Chain: a, b, c, d. Synonym: cytochrome c6 like protein, soluble cytochrome f, cytochrome c553, cytochromE C-553, cytochromE C-552, atc6. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: atc6. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.50Å R-factor: 0.188 R-free: 0.215

Authors:

H.Chida,T.Yokoyama,F.Kawai,A.Nakazawa,H.Akazaki,Y.Takayama,T.Hirano, K.Suruga,T.Satoh,S.Yamada,R.Kawachi,S.Unzai,T.Nishio,S.-Y.Park,T.Oku

Key ref:

H.Chida et al. (2006). Crystal structure of oxidized cytochrome c(6A) from Arabidopsis thaliana. FEBS Lett, 580, 3763-3768. PubMed id: 16777100 DOI: 10.1016/j.febslet.2006.05.067

Date:

11-Mar-06 Release date: 04-Jul-06

Protein chains

Q93VA3  (CYC6_ARATH) -  Cytochrome c6, chloroplastic from Arabidopsis thaliana

Seq: 175 a.a.

Struc: 102 a.a.

DOI no: 10.1016/j.febslet.2006.05.067

FEBS Lett 580:3763-3768 (2006)

PubMed id: 16777100

Crystal structure of oxidized cytochrome c(6A) from Arabidopsis thaliana.

H.Chida, T.Yokoyama, F.Kawai, A.Nakazawa, H.Akazaki, Y.Takayama, T.Hirano, K.Suruga, T.Satoh, S.Yamada, R.Kawachi, S.Unzai, T.Nishio, S.Y.Park, T.Oku.

ABSTRACT

Compared with algal and cyanobacterial cytochrome c(6), cytochrome c(6A) from higher plants contains an additional loop of 12 amino acid residues. We have determined the first crystal structure of cytochrome c(6A) from Arabidopsis thaliana at 1.5 Angstrom resolution in order to help elucidate its function. The overall structure of cytochrome c(6A) follows the topology of class I c-type cytochromes in which the heme prosthetic group covalently binds to Cys16 and Cys19, and the iron has octahedral coordination with His20 and Met60 as the axial ligands. Two cysteine residues (Cys67 and Cys73) within the characteristic 12 amino acids loop form a disulfide bond, contributing to the structural stability of cytochrome c(6A). Our model provides a chemical basis for the known low redox potential of cytochrome c(6A) which makes it an unsuitable electron carrier between cytochrome b(6)f and PSI.

Selected figure(s)

Figure 1.
Fig. 1. Crystal structure and electron-density map (2F[o] − F[c]) of cytochrome c[6A] from Arabidopsis thaliana. (A) The four protein molecules in the asymmetric unit of A. thaliana cytochrome c[6A]. (B) Final electron-density map around the zinc ion and neighboring residues contoured at 1.2 σ. (C) Cross-eyes stereo image of the overall strucrure of A. thaliana cytochrome c[6A]. (D) Superimposion of A. thaliana cytochrome c[6A] (red) and red alga P. yezoensis cytochrome c[6A] (blue). (E) The final electron-density map (2F[o] − F[c]) around the characteristic 12 amino acids loop contoured at 1.2 σ. A is represented by a Cα trace with an attached heme group. Four protein molecules were displayed by one molecule with a different color (red, green, yellow and cyan), respectively. The zinc is represented by sphere model with gray color. B and E the heme and amino acid residues are represented by ball-and-stick models with atom-specific colors: yellow, carbon; cyan, nitrogen; red, oxygen; orange, iron; green, sulfur; gray, zinc. C, The α-helices (blue), β-sheet (green) and the characteristic 12 amino acids loop (red) are indicated as thick ribbons. The Cys16, Cys19, His20, Met60, Cys67, Cys73 and heme are represented by ball-and-stick in the same coloring scheme as B and E. D, The superimposition was calculated using lsqkab in CCP4. The structure is superimposed by a rigid body rotation and translation that minimized the root-mean-square difference between their main chain Cα atoms.

Figure 2.
Fig. 2. The final electron-density map (2F[o] − F[c]) around the heme contoured at 1.2 σ. The heme and amino acid residues are represented by ball-and-stick models in the same coloring scheme as Fig. 1B, C and E.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2006, 580, 3763-3768) copyright 2006.

Figures were selected by the author.