6K40 image
Deposition Date 2019-05-22
Release Date 2020-05-27
Last Version Date 2023-11-22
Entry Detail
PDB ID:
6K40
Keywords:
Title:
Crystal structure of alkyl hydroperoxide reductase from D. radiodurans R1
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.27 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Alkyl hydroperoxide reductase AhpD
Gene (Uniprot):DR_1765
Chain IDs:A, B, C, D, E, F (auth: G), G (auth: F), H, I, J, K, L
Chain Length:197
Number of Molecules:12
Biological Source:Deinococcus radiodurans R1
Primary Citation
Crystal structure of the AhpD-like protein DR1765 from Deinococcus radiodurans R1.
Biochem.Biophys.Res.Commun. 529 444 449 (2020)
PMID: 32703449 DOI: 10.1016/j.bbrc.2020.06.061

Abstact

Deinococcus radiodurans is well known for its extreme resistance to ionizing radiation (IR). Since reactive oxygen species generated by IR can damage various cellular components, D. radiodurans has developed effective antioxidant systems to cope with this oxidative stress. dr1765 from D. radiodurans is predicted to encode an alkyl hydroperoxidase-like protein (AhpD family), which is implicated in the reduction of hydrogen peroxide (H2O2) and organic hydroperoxides. In this study, we constructed a dr1765 mutant strain (Δdr1765) and examined the survival rate after H2O2 treatment. Δdr1765 showed a significant decrease in the H2O2 resistance compared to the wild-type strain. We also determined the crystal structure of DR1765 at 2.27 Å resolution. DR1765 adopted an all alpha helix protein fold representative of the AhpD-like superfamily. Structural comparisons of DR1765 with its structural homologues revealed that DR1765 possesses the Glu74-Cys86-Tyr88-Cys89-His93 signature motif, which is conserved in the proton relay system of AhpD. Complementation of Δdr1765 with dr1765 encoding C86A or C89A mutation failed to restore the survival rate to wild-type level. Taken together, these results suggest that DR1765 might function as an AhpD to protect cells from oxidative stress.

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