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1 Joan and Sanford I. Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, USA
2 Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
Reprint requests to: Dimitar B. Nikolov, Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA; e-mail: dimitar{at}ximpact3.ski.mskcc.org; fax: (212) 717-3135.
(RECEIVED August 15, 2003; FINAL REVISION August 15, 2003; ACCEPTED August 18, 2003)
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03375603.
| Abstract |
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Keywords: Organic hydroperoxides; peroxiredoxins; peroxidase
| Introduction |
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The Ohr/OsmC proteins were identified as a family of bacterial proteins involved in the detoxification of organic hydroperoxides (Mongkolsuk et al. 1998; Atichartpongkul et al. 2001). They share no sequence homology to other prokaryotic or eukaryotic proteins. The sequence identity within each of the Ohr and OsmC subfamilies is between 40%70%, and ~20% between the two subfamilies (Fig. 1A
). Their more conserved carboxy-terminal region contains two invariant cysteine residues that play a critical role in hydroperoxide detoxification (Lesniak et al. 2002).
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| Results and Discussion |
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-helices (H2, H3, H4), whereas the smaller amino-terminal subdomain consists only of a three-stranded antiparallel ß-sheet (strands S1, S2, and S3) and one 310 helix (H1).
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Structural comparison between OsmC and Ohr
Overall, both the tertiary and quaternary structures of Ohr and OsmC are very similar. Superposition of the two molecules results in a root-mean-square deviation (rmsd) of 1.47 Å for 105
carbon positions (Fig. 2C
). The main structural differences between the two proteins involve rearrangements of secondary structural elements away from the active sites. The seven amino-terminal amino acids in Ohr form an extended coil that wraps around the other monomer, whereas in OsmC they are structured into a longer, more extended ß-strand S1. The second difference between the two structures involves ß-strands S1 and S2, which are longer in OsmC than in Ohr. A third difference is that helix H3 (OsmC amino acids 111123) is positioned further away from the enzymes core region in OsmC than in Ohr (displacements in this region ranging from 3.45 Å to 2.78 Å). Fourth, the loop region (OsmC amino acids 131134) linking helix H4 and ß-strand S6 in the proteins is substantially more tightly folded and compact in OsmC. Finally, the strand S6 of OsmC is longer than the one found in Ohr.
The active site residues (indicated with
in Fig. 1A
) of both enzymes are conserved and similarly positioned, including Pro48 (Pro49 in Ohr), Phe60 (Phe61 in Ohr), Glu49 (Glu50 in Ohr), and Ser128 (Ser127 in Ohr). One exception is the orientation and position of the side chain of Arg39, which in OsmC hydrogen bonds with Cys59 (S) (3.2 Å), but does not form a salt bridge with Glu49. In contrast, in Ohr, the functionally equivalent Arg18 both hydrogen bonds with the corresponding Cys60 (3.4 Å), and forms a salt bridge with Glu50. The Arg18Cys60 interaction has been shown, using site-directed mutagenesis, to be important for optimal catalytic activity of Ohr, presumably by lowering the pKa of the attacking Cys60 thiol (Lesniak et al. 2002). It is interesting that the proteins from the OsmC subfamily lack Arg18, which is fully conserved in the Ohr subfamily (marked with
in Fig. 1A
), but have created the same spatial arrangement of catalytic residues by using Arg39, which is in turn completely conserved in the OsmC subfamily. Position 18 (Arg in Ohr; Gly in OsmC) is located in the beginning of strand S2, whereas position 39 (Gly in Ohr; Arg in OsmC) is at the end of the nearby helix H1, therefore the side chain of an arginine at any of these two locations would easily fall within the hydrogen-binding distance to the attacking Cys59 and Cys60 in OsmC and Ohr, respectively.
Enzymatic activity of OsmC toward peroxide substrates
Recombinant OsmC was tested for peroxidase activity toward both inorganic (H2O2) and organic hydroperoxide (CHP) using a colorimetric FOX assay, as previously described (Lesniak et al. 2002). The results presented in Fig. 3AD
show that H2O2 and CHP can both serve as OsmC substrates. Nevertheless, the enzymes ability to turn these compounds over differs substantially. H2O2 is a relatively poor OsmC substrate: 10 µM of OsmC can remove ~13 µM of H2O2 in a minute, whereas only 3 µM of OsmC can metabolize >2000 µM CHP during the same time period. In addition, it takes >700 sec for 1 µM OsmC to process ~20 µM H2O2, but only 12 sec for the equivalent amount of CHP. These results are similar to the ones previously reported by us for Ohr, and are consistent with an apparent Km value for H2O2 in the 200800 µM range, and an approximately two-order of magnitude lower Km for CHP, demonstrating that both proteins evolved to detoxify organic peroxide substrates and not H2O2.
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Briefly, the activated Cys59 reacts with peroxide (ROOH) and is oxidized to a cysteine sulfenic acid (Cys59SOH) intermediate, whereas the peroxide is reduced to alcohol (ROH). Second, the Cys59SOH condenses with the Cys125 thiol located in the immediate vicinity, leading to the formation of an intramolecular disulfide bond and release of water. Finally, the oxidized OsmC is regenerated back to its enzymatically active, reduced state using an unidentified endogenous reductant R(SH)2.
Cussiol et al. (2003) have recently provided evidence that purified Xylella fastidiosa Ohr can be reduced back to its enzymatically active state by dihydrolipoic acid (DHLA), which would suggest that the protein is a dihydrolipoic acid peroxidase. This would also probably be true for the E. coli homolog. E. coli genome encodes enzymes necessary for the synthesis of DHLA: dihydrolipoamide succinyltransferase (GenBank ID: AAG55051 [GenBank] ), dihydrolipoamide dehydrogenase (GenBank ID: AAG54420 [GenBank] .1), and lipoate synthase (GenBank ID: AAG54962 [GenBank] .1).
Some bacteria express both Ohr and OsmC proteins, despite the fact that they are structurally and functionally similar. There are two plausible, and not mutually exclusive, explanations for this. First, it is possible that each protein resides in a distinct subcellular location, which may be beneficial, if, for example, one is primarily responsible for detoxification of exogenous peroxides produced by the host immune system, whereas the other inactivates the peroxide byproducts of bacterial metabolism. Second, it is possible that Ohr and OsmC have evolved to target different subsets of substrates. The OsmC structure suggests that the second possibility is probably true. Although both OsmC and Ohr proteins show a strong preference for the metabolism of organic hydroperoxides (tert-butyl and CHP) over an inorganic H2O2, the active site of OsmC and the surrounding surface region shows different distribution of hydrophobic residues from that of Ohr (Fig. 2D
). In addition, the overall three-dimensional shape of the active site cavities differs between the two enzymes. Whereas the active site of Ohr is relatively wide, the one in OsmC is more elongated and narrow (Fig. 2D
). Thus, OsmC and Ohr may be responsible for the detoxification of structurally different, albeit still hydrophobic peroxide substrates. Understanding of the precise biological role of Ohr and OsmC would require identification of the endogenous substrates for each enzyme, and careful characterization of the kinetic parameters for each substrate. Finally, unlike other peroxidases, both the Ohr and OsmC hydroperoxide reductase subfamilies are present only in bacteria (most of which are pathogenic to plants and humans), and therefore, could potentially represent viable therapeutic drug targets.
The atomic coordinates and structure factors have been deposited in the Protein Data Bank under the code 1QWI.
| Materials and methods |
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| Acknowledgments |
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The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.
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