PDBsum entry 1i6d

Electron transport

PDB id: 1i6d

Contents

Protein chain

100 a.a. *

Ligands

HEC

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Solution structure and dynamics of the functional domain of paracoccus denitrificans cytochrome c(552) in both redox states.

Authors

B.Reincke, C.Pérez, P.Pristovsek, C.Lücke, C.Ludwig, F.Löhr, V.V.Rogov, B.Ludwig, H.Rüterjans.

Ref.

Biochemistry, 2001, 40, 12312-12320. [DOI no: 10.1021/bi010615o]

PubMed id

11591150

Abstract

A soluble and fully functional 10.5 kDa fragment of the 18.2 kDa membrane-bound cytochrome c(552) from Paracoccus denitrificans has been heterologously expressed and (13)C/(15)N-labeled to study the structural features of this protein in both redox states. Well-resolved solution structures of both the reduced and oxidized states have been determined using high-resolution heteronuclear NMR. The overall protein topology consists of two long terminal helices and three shorter helices surrounding the heme moiety. No significant redox-induced structural differences have been observed. (15)N relaxation rates and heteronuclear NOE values were determined at 500 and 600 MHz. Several residues located around the heme moiety display increased backbone mobility in both oxidation states, while helices I, III, and V as well as the two concatenated beta-turns between Leu30 and Arg36 apparently form a less flexible domain within the protein structure. Major redox-state-dependent differences of the internal backbone mobility on the picosecond-nanosecond time scale were not evident. Hydrogen exchange experiments demonstrated that the slow-exchanging amide proton resonances mainly belong to the helices and beta-turns, corresponding to the regions with high order parameters in the dynamics data. Despite this correlation, the backbone amide protons of the oxidized cytochrome c(552) exchange considerably faster with the solvent compared to the reduced protein. Using both differential scanning calorimetry as well as temperature-dependent NMR spectroscopy, a significant difference in the thermostabilities of the two redox states has been observed, with transition temperatures of 349.9 K (76.8 degrees C) for reduced and 307.5 K (34.4 degrees C) for oxidized cytochrome c(552). These results suggest a clearly distinct backbone stability between the two oxidation states.

Secondary reference #1

Title

Solution structure of the functional domain of paracoccus denitrificans cytochrome c552 in the reduced state.

Authors

P.Pristovsek, C.Lücke, B.Reincke, B.Ludwig, H.Rüterjans.

Ref.

Eur J Biochem, 2000, 267, 4205-4212. [DOI no: 10.1046/j.1432-1327.2000.01456.x]

PubMed id

10866825

Figure 4.
Fig. 4. Schematic representation of therefined solution structure in the reduced state of cytochrome c[552] from Paracoccus denitrificans. (Produced with MOLSCRIPT [47] and Raster3D [48].

Figure 5.
Fig. 5. Solvent accessible surface of cytochrome c[552] from Paracoccus denitrificans in the reduced state (A, front view; B, rear view). Lysine residues are depicted in black, the heme in gray.

The above figures are reproduced from the cited reference with permission from the Federation of European Biochemical Societies

Secondary reference #2

Title

Structure of the soluble domain of cytochrome c(552) from paracoccus denitrificans in the oxidized and reduced states.

Authors

A.Harrenga, B.Reincke, H.Rüterjans, B.Ludwig, H.Michel.

Ref.

J Mol Biol, 2000, 295, 667-678. [DOI no: 10.1006/jmbi.1999.3382]

PubMed id

10623555

Figure 2.
Figure 2. Overview of the four cytochromes c[552]' in the asymmetric unit. Molecule A, light blue; molecule B, green; molecule C, yellow; molecule D, magenta. The bound water molecules are shown as blue spheres. The Figure was prepared using the program SETOR [Evans 1993].

Figure 6.
Figure 6. Schematic representation of the polar interactions (hydrogen bonds and ion pairs) with the heme propionates of cytochrome c[552]'(broken lines). The two thioether linkages are shown in green. The nomenclature used for the amino acid residues and heme atoms follows the conventions of the Protein Data Bank. The Figure was prepared using LIGPLOT [Wallace et al 1995], MOLSCRIPT [Kraulis 1991] and RASTER3D [Merrit and Murphy 1994].

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #3

Title

Heterologous expression of soluble fragments of cytochrome c552 acting as electron donor to the paracoccus denitrificans cytochrome c oxidase.

Authors

B.Reincke, L.Thöny-Meyer, C.Dannehl, A.Odenwald, M.Aidim, H.Witt, H.Rüterjans, B.Ludwig.

Ref.

Biochim Biophys Acta, 1999, 1411, 114-120. [DOI no: 10.1016/S0005-2728(99)00037-7]

PubMed id

10216157