PDBsum entry 2fwf

Oxidoreductase

PDB id: 2fwf

Contents

Protein chain

123 a.a. *

Metals

_NA ×2

IOD ×7

Waters ×172

* Residue conservation analysis

PDB id:

2fwf

Name:

Oxidoreductase

Title:

High resolution crystal structure of thE C-terminal domain of the electron transfer catalyst dsbd (reduced form)

Structure:

Thiol:disulfide interchange protein dsbd. Chain: a. Fragment: c-terminal domain, residues 419-546. Synonym: protein-disulfide reductase, disulfide reductase, c-type cytochrome biogenesis protein cycz, inner membrane copper tolerance protein. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: dsbd, dipz, cycz, cuta2, b4136. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.30Å R-factor: 0.170 R-free: 0.196

Authors:

C.U.Stirnimann,A.Rozhkova,U.Grauschopf,R.A.Boeckmann,R.Glockshuber, G.Capitani,M.G.Gruetter

Key ref:

C.U.Stirnimann et al. (2006). High-resolution structures of Escherichia coli cDsbD in different redox states: A combined crystallographic, biochemical and computational study. J Mol Biol, 358, 829-845. PubMed id: 16545842 DOI: 10.1016/j.jmb.2006.02.030

Date:

02-Feb-06 Release date: 13-Jun-06

Protein chain

P36655  (DSBD_ECOLI) -  Thiol:disulfide interchange protein DsbD from Escherichia coli (strain K12)

Seq: 565 a.a.

Struc: 123 a.a.

Enzyme reactions

• Enzyme class: E.C.1.8.1.8 - protein-disulfide reductase.
• Reaction:
  1. [protein]-dithiol + NAD⁺ = [protein]-disulfide + NADH + H⁺
  2. [protein]-dithiol + NADP⁺ = [protein]-disulfide + NADPH + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2006.02.030

J Mol Biol 358:829-845 (2006)

PubMed id: 16545842

High-resolution structures of Escherichia coli cDsbD in different redox states: A combined crystallographic, biochemical and computational study.

C.U.Stirnimann, A.Rozhkova, U.Grauschopf, R.A.Böckmann, R.Glockshuber, G.Capitani, M.G.Grütter.

ABSTRACT

Escherichia coli DsbD transports electrons from cytoplasmic thioredoxin to periplasmic target proteins. DsbD is composed of an N-terminal (nDsbD) and a C-terminal (cDsbD) periplasmic domain, connected by a central transmembrane domain. Each domain possesses two cysteine residues essential for electron transport. The transport proceeds via disulfide exchange reactions from cytoplasmic thioredoxin to the central transmembrane domain and via cDsbD to nDsbD, which then reduces the periplasmic target proteins. We determined four high-resolution structures of cDsbD: oxidized (1.65 A resolution), chemically reduced (1.3 A), photo-reduced (1.1 A) and chemically reduced at pH increased from 4.6 to 7. The latter structure was refined at 0.99 A resolution, the highest achieved so far for a thioredoxin superfamily member. The data reveal unprecedented structural details of cDsbD, demonstrating that the domain is very rigid and undergoes hardly any conformational change upon disulfide reduction or interaction with nDsbD. In full agreement with the crystallographic results, guanidinium chloride-induced unfolding and refolding experiments indicate that oxidized and reduced cDsbD are equally stable. We confirmed the structural rigidity of cDsbD by molecular dynamics simulations. A remarkable feature of cDsbD is the pKa of 9.3 for the active site Cys461: this value, determined using two different experimental methods, surprisingly was around 2.5 units higher than expected on the basis of the redox potential. Additionally, taking advantage of the very high quality of the cDsbD structures, we carried out pKa calculations, which gave results in agreement with the experimental findings. In conclusion, our wide-scope analysis of cDsbD, encompassing atomic-resolution crystallography, computational chemistry and biophysical measurements, highlighted two so far unrecognized key aspects of this domain: its unusual redox properties and extreme rigidity. Both are likely to be correlated to the role of cDsbD as a covalently linked electron shuttle between the membrane domain and the N-terminal periplasmic domain of DsbD.

Selected figure(s)

Figure 2.
Figure 2. Mechanism of disulfide opening in crystals induced by synchrotron radiation (adapted from Weik et al.37 and Fauvodon et al.40).

Figure 6.
Figure 6. Reduced DsbA active site (green and atom colors) superimposed onto the active site of cDsbD[red] (magenta and atom colors).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 829-845) copyright 2006.

Figures were selected by an automated process.