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PDBsum entry 2dge
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Electron transport
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PDB id
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2dge
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References listed in PDB file
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Key reference
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Title
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Crystal structure of oxidized cytochrome c(6a) from arabidopsis thaliana.
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Authors
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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.
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Ref.
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FEBS Lett, 2006,
580,
3763-3768.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
FEBS Lett
(2006,
580,
3763-3768)
copyright 2006.
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