PDBsum entry 2v3b

Oxidoreductase

PDB id: 2v3b

Contents

Protein chains

381 a.a. *

53 a.a. *

Ligands

FAD

Metals

_FE

Waters ×255

* Residue conservation analysis

PDB id:

2v3b

Name:

Oxidoreductase

Title:

Crystal structure of the electron transfer complex rubredoxin - rubredoxin reductase from pseudomonas aeruginosa.

Structure:

Rubredoxin reductase. Chain: a. Engineered: yes. Rubredoxin 2. Chain: b. Synonym: rubredoxin. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: pao1. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Resolution:

2.45Å R-factor: 0.185 R-free: 0.246

Authors:

G.Hagelueken,L.Wiehlmann,T.M.Adams,H.Kolmar,D.W.Heinz,B.Tuemmler,W.- D.Schubert

Key ref:

G.Hagelueken et al. (2007). Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A, 104, 12276-12281. PubMed id: 17636129 DOI: 10.1073/pnas.0702919104

Date:

14-Jun-07 Release date: 14-Aug-07

Protein chain

Q9HTK9  (RURE_PSEAE) -  Rubredoxin-NAD(+) reductase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 384 a.a.

Struc: 381 a.a.

Protein chain

Q9HTK8  (RUBR2_PSEAE) -  Rubredoxin-2 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 55 a.a.

Struc: 53 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.1.18.1.1 - rubredoxin--NAD(+) reductase.
• Reaction: 2 reduced [rubredoxin] + NAD⁺ + H⁺ = 2 oxidized [rubredoxin] + NADH
• Cofactor: FAD; Fe cation

FAD (Bound ligand (Het Group name = FAD) corresponds exactly) Fe cation

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

reference

DOI no: 10.1073/pnas.0702919104

Proc Natl Acad Sci U S A 104:12276-12281 (2007)

PubMed id: 17636129

Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa.

G.Hagelueken, L.Wiehlmann, T.M.Adams, H.Kolmar, D.W.Heinz, B.Tümmler, W.D.Schubert.

ABSTRACT

Crude oil spills represent a major ecological threat because of the chemical inertness of the constituent n-alkanes. The Gram-negative bacterium Pseudomonas aeruginosa is one of the few bacterial species able to metabolize such compounds. Three chromosomal genes, rubB, rubA1, and rubA2 coding for an NAD(P)H:rubredoxin reductase (RdxR) and two rubredoxins (Rdxs) are indispensable for this ability. They constitute an electron transport (ET) pathway that shuttles reducing equivalents from carbon metabolism to the membrane-bound alkane hydroxylases AlkB1 and AlkB2. The RdxR-Rdx system also is crucial as part of the oxidative stress response in archaea or anaerobic bacteria. The redox couple has been analyzed in detail as a model system for ET processes. We have solved the structure of RdxR of P. aeruginosa both alone and in complex with Rdx, without the need for cross-linking, and both structures were refined at 2.40- and 2.45-A resolution, respectively. RdxR consists of two cofactor-binding domains and a C-terminal domain essential for the specific recognition of Rdx. Only a small number of direct interactions govern mutual recognition of RdxR and Rdx, corroborating the transient nature of the complex. The shortest distance between the redox centers is observed to be 6.2 A.

Selected figure(s)

Figure 2.
Fig. 2. Structure of the Rdx–RdxR complex. (A) Cartoon representation. RdxR colors are as in Fig. 1A, and Rdx is in dark red. FAD, modeled NADH (translucent), and cysteine residues of the iron-binding site are shown in ball-and-stick mode, and Fe^3+ is shown as a green sphere. Anomalous-difference electron density (red) contoured at 6.0 documents the presence of the Fe^3+. Amino acid exchanges between RubA1 and RubA2 are indicated as spheres in Rdx (conservative, orange; nonconservative, blue). (B) Interactions surrounding the redox-active site of the complex. Interacting residues are shown as ball-and-stick models (C of RdxR, yellow, and of Rdx, red-brown). FAD is shown in ball-and-stick mode. (C) Binding curves for the interaction of RdxR to Fe^3+ (red)- and Ni^2+ (green)-substituted Rdx.

Figure 3.
Fig. 3. Phylogenetic topology of structurally characterized enzymes functionally and/or structurally related to RdxR. (A) FNR, plant-type ferredoxin reductase; AdxR, adrenodoxin reductase; AIF, apoptosis inducing factor; LpdR, lipoamide reductase; TptR, trypanothione reductase. Sequence identity to RdxR is indicated by percentage. (B) Superposition of uncomplexed (gray) and complexed RdxR (colored as in Fig. 1A). Cofactors are shown as ball-and-stick models. For clarity, the position of Rdx is indicated by a brown sphere. (C) Comparison of the Rdx (red) and Trx (black) binding sites of RdxR and TrxR. For clarity, only the molecular surface of RdxR is shown. G^0 optimized ET rates (42) between FAD and each point of the RdxR surface are indicated by a color gradient (red, high ET rate; green, medium; blue, low). (Inset) Close-up view of the cofactors involved.

Figures were selected by the author.

Author's comment

Crude oil spills represent a major ecological threat due to the chemical inertness of the constituent n-alkanes. The Gram-negative bacterium Pseudomonas aeruginosa is one of the few bacterial species able to metabolize such compounds. Three chromosomal genes, rubB, rubA1 and rubA2 coding for an NAD(P)H:rubredoxin oxidoreductase (RdxR) and two rubredoxins (Rdxs) are indispensable for this ability. They constitute an electron transport (ET) pathway that shuttles reducing equivalents from carbon metabolism to the membrane-bound alkane hydroxylases AlkB1 and AlkB2. The RdxR/Rdx system is also crucial as part of the oxidative stress response in archaea or anaerobic bacteria. The redox couple has been analyzed in detail as a model system for ET processes. The crystal structure of RdxR, refined at 2.40 resolution, reveals two domains, a cofactor-binding domains and a C-terminal domain essential for the specific recognition of Rdx. The crystal structure of the RdxR/Rdx complex refined at 2.45Å indicates that mutual recognition is governed by a small number of direct interactions, corroborating the transient nature of the complex. The shortest distance between the redox centers is observed to be 6.2Å.