Crystal structure of the C47S mutant of human peroxiredoxin 5

Abstract

In the crystal structure of the reduced form of the wild-type human peroxiredoxin 5, the presence of a benzoate ion in direct interaction with the peroxidatic cysteine (Cys 47) appeared as a rather intriguing feature since it is known that the benzoate ion can play the role of a specific hydroxyl radical scavenger. The crystal structure of the C47S mutant of the same enzyme has been crystallized in the tetragonal system, space group P4 1 2 1 2, with a = 65.65 Å, c = 122.04 Å. It confirms the presence of this benzoate ion in spite of the mutation into a serine of the Cys 47 residue to which the benzoate ion was directly linked in the wild-type structure. The benzoate ion seems to be stabilized by hydrophobic contacts on both sides of the aromatic ring. In this matter, the α5 helix, which is specific to peroxiredoxin 5 among mammalian peroxiredoxins, plays an important role. These hydrophobic contacts also allow to suggest why the benzoate ion disappears when the molecule is oxidized.

Structural Changes Common to Catalysis in the Tpx Peroxiredoxin Subfamily

“…The protein adopts the FF conformation (Figure 3A and B), but it is slightly distorted as the crystal packing places the C-terminal carboxylate from Ala168 of a symmetry mate in the active site, hydrogen bonded to Thr58 and Arg133 (Figure 2B). Although the terminal carboxylate could mimic peroxide binding as has been seen for other Prxs with bound benzoate 4,26,27,28,29 , ethanediol 30 , or acetate 31 , neither oxygen atom is close enough to the C P to approximate the binding of substrate.…”

Crystal Structure of an Archaeal Peroxiredoxin from the Aerobic Hyperthermophilic Crenarchaeon Aeropyrum pernix K1

“…The C207 and C R 213 residues reside on b10 and b11, respectively, which construct a b-hairpin motif. Such an intra-monomer disulfide linkage has not been observed in other Prx structures, [16][17][18][19][20][21][22][23][30][31][32][33][34][35][36][37] and it must be a common structural characteristic of the many archaeal Prxs that conserve two cysteine residues within the unique primary sequence motif CXDWWFC in the archaeal C-terminal region (Figure 1). Since the intra-cellular environment is generally reducing conditions and the intra-monomer C207-S-S-C R 213 is exposed to the bulk solvent in the crystal structure, it is not obvious whether the intramonomer C207-S-S-C R 213 formation could occur under the usual physiological conditions.…”

“…15 The Prx superfamily members can be divided into seven subfamilies, depending on their primary sequence characteristics ( Figure 1): (i) typical 2-Cys Prxs; [16][17][18][19][20][21][22] (ii) 1-Cys Prxs; 15,23 (iii) archaeal Prxs, 24,25 which are distributed mainly in archaea but are present also in several microorganisms; (iv) Bcp Prxs, [26][27][28] which are one class of Prx homologues that were identified originally as bacterioferritin comigratory protein (Bcp); (v) Tpx Prxs, [29][30][31] which are homologues of bacterial periplasmic thiol peroxidase (Tpx); (vi) hybrid Prxs, 32 in which a glutaredoxin domain is fused after the Prx domain; and (vii) type-II Prxs. [33][34][35][36][37] Recently, an archaeal Prx consisting of 250 amino acid residues per monomer (molecular mass 28,703 Da) from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1 has been characterized. 24 The A. pernix archaeal Prx shares primary sequence similarity with the 1-Cys Prxs ( Figure 1).…”

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

“…The side chain of Arg151 is not in direct contact with Ser45 O γ but also lies in the vicinity. In the wild‐type enzyme, the surroundings of Cys45 would thus be very similar to what is observed in other PRDXs, with the exception of the benzoate ion, which was observed only in the crystal structure of human PRDX5 (Declercq and Evrard 2001; Declercq et al 2001; Evrard et al 2004a) and in the C47S mutant of the same enzyme (Evrard et al 2004b). As can be seen on the structural alignment presented in Table 1, Arg128 and Thr42 are conserved in all the PRDXs presented here, while the equivalent of His37 is missing only in human PRDX2.…”