PDBsum entry: 1fl2

Oxidoreductase

PDB id: 1fl2

Contents

Protein chain

310 a.a. *

Ligands

SO4 ×5

FAD

Waters ×409

* Residue conservation analysis

PDB id:

1fl2

Name:

Oxidoreductase

Title:

Catalytic core component of the alkylhydroperoxide reductase e.Coli

Structure:

Alkyl hydroperoxide reductase subunit f. Chain: a. Fragment: c-terminal domain. Synonym: alkyl hydroperoxide reductase f52a protein. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.197 R-free: 0.217

Authors:

B.Bieger,L.-O.Essen

Key ref:

B.Bieger and L.O.Essen (2001). Crystal structure of the catalytic core component of the alkylhydroperoxide reductase AhpF from Escherichia coli. J Mol Biol, 307, 1-8. PubMed id: 11243797 DOI: 10.1006/jmbi.2000.4441

Date:

11-Aug-00 Release date: 21-Mar-01

Protein chain

P35340  (AHPF_ECOLI) -  Alkyl hydroperoxide reductase subunit F

Seq: 521 a.a.

Struc: 310 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (1 term)
• Biochemical function: oxidoreductase activity (4 terms)

DOI no: 10.1006/jmbi.2000.4441

J Mol Biol 307:1-8 (2001)

PubMed id: 11243797

Crystal structure of the catalytic core component of the alkylhydroperoxide reductase AhpF from Escherichia coli.

B.Bieger, L.O.Essen.

ABSTRACT

Alkylhydroperoxide reductases (AhpR, EC 1.6.4.*) are essential for the oxygen tolerance of aerobic organisms by converting otherwise toxic hydroperoxides of lipids or nucleic acids to the corresponding alcohols. The AhpF component belongs to the family of pyridine nucleotide-disulphide oxidoreductases and channels electrons from NAD(P)H towards the AhpC component which finally reduces cognate substrates. The structure of the catalytic core of the Escherichia coli AhpF (A212-A521) with a bound FAD cofactor was determined at 1.9 A resolution in its oxidized state. The dimeric arrangement of the AhpF catalytic core and the predicted interaction mode between the N-terminal PDO-like domain and the NADPH domain favours an intramolecular electron transfer between the two redox-active disulphide centres of AhpF.

Selected figure(s)

Figure 1.
Figure 1. (a) Ribbon diagram of the oxidized form of the catalytic core of AhpF (residues R210-A521) with the FAD cofactor bound in the FAD-domain and the oxidized disulphide centre C345-C348 located on the NADPH-domain. Interestingly, three of the five observed sulphate anions are appropriately placed to cap the helix dipoles of a5, and the 3[10]-helices G334-Y337, N456-E459 at their corresponding N termini. (b) The AhpF homodimer viewed along the 2-fold symmetry axis. The two FAD cofactors are indicated as ball-and-stick models. The N termini of each AhpF monomer are located at opposite ends of the homodimer. This observation was used for the discrimination between an inter- or intramolecular electron transfer from C345-C348 to the N-terminal disulphide centre C129-C132, as described in the text. This Figure and Figure 2 and Figure 3 were made with MOLSCRIPT [24] and Raster3D. [25]

Figure 3.
Figure 3. (a) Sketch of the hypothetical intramolecular mechanism for the electron transfer reaction from the primary disulphide C345-C348 to the secondary disulphide C129-C132. The second monomer of the AhpF dimer is not shown for easier visualization. The mechanism was derived from manual docking experiments which were carried out with the E. coli AhpF catalytic core and a model of the N terminus PDO-like domain of AhpF comprising the disulphide centre C129-C132. Only in the reduced state, can C129-C132 of the PDO-like domain (blue) approach C348 of the NADPH domain (green), while in the oxidized state, the cysteine residues C345 and C348 are occluded between the NADPH and the FAD (red) domain. FAD and NADPH cofactors are shown as sticks, redox-active disulphides as space-filling models. (b) Overall shape complementarity between the PDO-like domain and the dimeric catalytic core of AhpF. The inlay shows the distances between the N and C termini in the docked state, while the right panel shows the PDO-like domain (blue) and the AhpF dimer (FAD domains, red and dark grey; NADPH domain, light grey). A sequence analysis by PSIBLAST[26] showed that the N-terminal region of AhpF is highly homologous to the PDO from P. furiosous (PDB entry 1A8L) with a sequence identity of 26 % and a PSIBLAST score of 6 × 10^ -51. Using this sequence alignment, a structural model of AhpF(1-200) was generated by MODELLER4.[27] The resulting model exhibits good stereochemistry as analysed by PROCHECK. [28] The PDO-like region of E. coli AhpF consists of two thioredoxin-like modules like the PDO from P. furiosous, but contains only one conserved disulphide centre (C129-C132) in the second TrX-like module, while in the first Trx-like module the cysteine residues found in PDO are replaced by serine (S30-S33). The docking of the AhpF PDO-like domain (M1-E200) was carried out using the graphical interface of InsightII (MSI).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 1-8) copyright 2001.

Figures were selected by an automated process.