PDBsum entry 2v41

Oxidoreductase

PDB id: 2v41

Contents

Protein chains

(+ 2 more) 220 a.a. *

Ligands

BEZ ×8

Waters ×294

* Residue conservation analysis

PDB id:

2v41

Name:

Oxidoreductase

Title:

Crystal structure of the c45s mutant of the peroxiredoxin 6 of arenicola marina. Orthorhombic form

Structure:

Peroxiredoxin 6.. Chain: a, b, c, d, e, f, g, h. Synonym: peroxiredoxin 6 of arenicola marina. Engineered: yes. Mutation: yes

Source:

Arenicola marina. Organism_taxid: 6344. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.180 R-free: 0.239

Authors:

A.Smeets,J.P.Declercq

Key ref:

A.Smeets et al. (2008). The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers. Protein Sci, 17, 700-710. PubMed id: 18359859 DOI: 10.1110/ps.073399308

Date:

27-Jun-07 Release date: 08-Apr-08

Protein chains

Q1AN22  (Q1AN22_AREMA) -  Peroxiredoxin 6 from Arenicola marina

Seq: 220 a.a.

Struc: 220 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.1.11.1.15 - Transferred entry: 1.11.1.24, 1.11.1.25, 1.11.1.26, 1.11.1.27, 1.11.1.28
• Pathway: Peroxiredoxin
• Reaction: 2 R'-SH + ROOH = R'-S-S-R' + H₂O + ROH

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

reference

DOI no: 10.1110/ps.073399308

Protein Sci 17:700-710 (2008)

PubMed id: 18359859

The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers.

A.Smeets, E.Loumaye, A.Clippe, J.F.Rees, B.Knoops, J.P.Declercq.

ABSTRACT

The peroxiredoxins (PRDXs) define a superfamily of thiol-dependent peroxidases able to reduce hydrogen peroxide, alkyl hydroperoxides, and peroxynitrite. Besides their cytoprotective antioxidant function, PRDXs have been implicated in redox signaling and chaperone activity, the latter depending on the formation of decameric high-molecular-weight structures. PRDXs have been mechanistically divided into three major subfamilies, namely typical 2-Cys, atypical 2-Cys, and 1-Cys PRDXs, based on the number and position of cysteines involved in the catalysis. We report the structure of the C45S mutant of annelid worm Arenicola marina PRDX6 in three different crystal forms determined at 1.6, 2.0, and 2.4 A resolution. Although A. marina PRDX6 was cloned during the search of annelid homologs of mammalian 1-Cys PRDX6s, the crystal structures support its assignment to the mechanistically typical 2-Cys PRDX subfamily. The protein is composed of two distinct domains: a C-terminal domain and an N-terminal domain exhibiting a thioredoxin fold. The subunits are associated in dimers compatible with the formation of intersubunit disulfide bonds between the peroxidatic and the resolving cysteine residues in the wild-type enzyme. The packing of two crystal forms is very similar, with pairs of dimers associated as tetramers. The toroid-shaped decamers formed by dimer association and observed in most typical 2-Cys PRDXs is not present. Thus, A. marina PRDX6 presents structural features of typical 2-Cys PRDXs without any formation of toroid-shaped decamers, suggesting that it should function more like a cytoprotective antioxidant enzyme or a modulator of peroxide-dependent cell signaling rather than a molecular chaperone.

Selected figure(s)

Figure 2.
(A) Accessible surface of a monomer colored according to the electrostatic potential: blue for positive, and red for negative. (B) Similar to A with the benzoate ion covering the active site pocket. (C) Details of the active site. Important residues discussed in the text are represented as balls and sticks. (D) Electron density in the region of the active site. The sigma map is contoured at a level of 1.0 [sigma].

Figure 4.
C^[alpha] traces of two monomers belonging to two different dimers in reduced human PRDX2 are represented by green and cyan, respectively. This association gives rise to the formation of the toroid-shaped decamer. Two monomers of A. marina PRDX6 superposed on the two monomers of PRDX2 are shown in red and blue, respectively. The region containing the short two-stranded [beta]-sheet ([beta]6, [beta]7) in A. marina PRDX6 is much bulkier than the equivalent region in PRDX2, and this kind of association is not allowed.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2008, 17, 700-710) copyright 2008.

Figures were selected by an automated process.