6E8L

Crystal Structure of Alkyl hydroperoxidase D (AhpD) from Streptococcus pneumoniae (Strain D39/ NCTC 7466)

Summary for 6E8L

• Entry DOI: 10.2210/pdb6e8l/pdb
• Descriptor: Alkyl hydroperoxide reductase AhpD (2 entities in total)
• Functional Keywords: alkylhydroperoxidase peroxiredoxin, oxidoreductase
• Biological source: Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)
• Total number of polymer chains: 6
• Total formula weight: 119120.44

Authors

Meng, Y.,Davies, J.,North, R.,Coombes, D.,Horne, C.,Hampton, M.,Dobson, R. (deposition date: 2018-07-30, release date: 2019-08-28, Last modification date: 2024-03-13)

Primary citation

Meng, Y.,Sheen, C.R.,Magon, N.J.,Hampton, M.B.,Dobson, R.C.J.
Structure-function analyses of alkylhydroperoxidase D fromStreptococcus pneumoniaereveal an unusual three-cysteine active site architecture.
J.Biol.Chem., 295:2984-2999, 2020

PubMed Abstract: During aerobic growth, the Gram-positive facultative anaerobe and opportunistic human pathogen generates large amounts of hydrogen peroxide that can accumulate to millimolar concentrations. The mechanism by which this catalase-negative bacterium can withstand endogenous hydrogen peroxide is incompletely understood. The enzyme alkylhydroperoxidase D (AhpD) has been shown to contribute to pneumococcal virulence and oxidative stress responses We demonstrate here that AhpD exhibits weak thiol-dependent peroxidase activity and, unlike the previously reported AhpC/D system, AhpD does not mediate electron transfer to AhpC. A 2.3-Å resolution crystal structure revealed several unusual structural features, including a three-cysteine active site architecture that is buried in a deep pocket, in contrast to the two-cysteine active site found in other AhpD enzymes. All single-cysteine AhpD variants remained partially active, and LC-MS/MS analyses revealed that the third cysteine, Cys-163, formed disulfide bonds with either of two cysteines in the canonical Cys-78--Cys-81 motif. We observed that AhpD formed a dimeric quaternary structure both in the crystal and in solution, and that the highly conserved Asn-76 of the AhpD core motif is important for AhpD folding. In summary, AhpD is a weak peroxidase and does not transfer electrons to AhpC, and therefore does not fit existing models of bacterial AhpD antioxidant defense mechanisms. We propose that it is unlikely that AhpD removes peroxides either directly or via AhpC, and that AhpD cysteine oxidation may act as a redox switch or mediate electron transfer with other thiol proteins.

PubMed: 31974167
DOI: 10.1074/jbc.RA119.012226

Experimental method

X-RAY DIFFRACTION (2.3 Å)