PDBsum entry 1upd

Electron transport

PDB id: 1upd

Contents

Protein chain

107 a.a. *

Ligands

HEC ×4

Waters ×147

* Residue conservation analysis

PDB id:

1upd

Name:

Electron transport

Title:

Oxidized structure of cytochrome c3 from desulfovibrio desulfuricans atcc 27774 at ph 7.6

Structure:

Cytochrome c3. Chain: a. Synonym: cytc3

Source:

Desulfovibrio desulfuricans. Organism_taxid: 876. Atcc: 27774

Resolution:

1.40Å R-factor: 0.147 R-free: 0.191

Authors:

I.Bento,P.M.Matias,A.M.Baptista,P.N.Da Costa,W.M.A.M.Van Dongen, L.M.Saraiva,T.R.Schneider,C.M.Soares,M.A.Carrondo

Key ref:

I.Bento et al. (2004). Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at pH 7.6. Proteins, 54, 135-152. PubMed id: 14705030 DOI: 10.1002/prot.10431

Date:

29-Sep-03 Release date: 30-Sep-04

Protein chain

Q9L915  (Q9L915_DESDE) -  Class III cytochrome C family protein from Desulfovibrio desulfuricans

Seq: 128 a.a.

Struc: 107 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1002/prot.10431

Proteins 54:135-152 (2004)

PubMed id: 14705030

Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at pH 7.6.

I.Bento, P.M.Matias, A.M.Baptista, P.N.da Costa, W.M.van Dongen, L.M.Saraiva, T.R.Schneider, C.M.Soares, M.A.Carrondo.

ABSTRACT

The tetraheme cytochrome c3 is a small metalloprotein with ca. 13,000 Da found in sulfate-reducing bacteria, which is believed to act as a partner of hydrogenase. The three-dimensional structure of the oxidized and reduced forms of cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774 at pH 7.6 were determined using high-resolution X-ray crystallography and were compared with the previously determined oxidized form at pH 4.0. Theoretical calculations were performed with both structures, using continuum electrostatic calculations and Monte Carlo sampling of protonation and redox states, in order to understand the molecular basis of the redox-Bohr and cooperativity effects related to the coupled transfer of electrons and protons. We were able to identify groups that showed redox-linked conformational changes. In particular, Glu61, His76, and propionate D of heme II showed important contributions to the redox-cooperativity, whereas His76, propionate A of heme I, and propionate D of heme IV were the key residues for the redox-Bohr effect. Upon reduction, an important movement of the backbone region surrounding hemes I and II was also identified, that, together with a few redox-linked conformational changes in side-chain residues, results in a significant decrease in the solvent accessibility of hemes I and II.

Selected figure(s)

Figure 2.
Figure 2. Stereoviews of heme II and its surroundings. a: Oxidized form at pH 4.0; b: oxidized form at pH 7.6; c: reduced form at pH 7.6.

Figure 5.
Figure 5. Stereoview of heme I. a: Oxidized form at pH 4.0; b: oxidized form at pH 7.6; c: reduced form at pH 7.6.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 54, 135-152) copyright 2004.

Figures were selected by an automated process.