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Open Access Research article

Crystal structure of alkyl hydroperoxidase D like protein PA0269 from Pseudomonas aeruginosa: Homology of the AhpD-like structural family

Teresa E Clarke1, Vladimir Romanov1, Yuri N Chirgadze2, Chananat Klomsiri3, Gera Kisselman1, Jean Wu-Brown1, Leslie B Poole3, Emil F Pai14 and Nickolay Y Chirgadze15*

Author Affiliations

1 Campbell Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada

2 Institute of Protein Research, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia

3 Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA

4 Departments of Biochemistry, Molecular Genetics, and Medical Biophysics, University of Toronto, Toronto, Ontario, Canada

5 Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada

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BMC Structural Biology 2011, 11:27  doi:10.1186/1472-6807-11-27

Published: 26 May 2011

Abstract

Background

Alkyl hydroperoxidase activity provides an important antioxidant defense for bacterial cells. The catalytic mechanism requires two peroxidases, AhpC and AhpD, where AhpD plays the role of an essential adaptor protein.

Results

The crystal structure of a putative AhpD from Pseudomonas aeruginosa has been determined at 1.9 Å. The protein has an all-helical fold with a chain topology similar to a known AhpD from Mycobacterium tuberculosis despite a low overall sequence identity of 9%. A conserved two α-helical motif responsible for function is present in both. However, in the P. aeruginosa protein, helices H3, H4 of this motif are located at the N-terminal part of the chain, while in M. tuberculosis AhpD, the corresponding helices H8, H9 are situated at the C-terminus. Residues 24-62 of the putative catalytic region of P. aeruginosa have a higher sequence identity of 33% where the functional activity is supplied by a proton relay system of five residues, Glu36, Cys48, Tyr50, Cys51, and His55, and one structural water molecule. A comparison of five other related hypothetical proteins from various species, assigned to the alkyl hydroperoxidase D-like protein family, shows they contain the same conserved structural motif and catalytic sequence Cys-X-X-Cys. We have shown that AhpD from P. aeruginosa exhibits a weak ability to reduce H2O2 as tested using a ferrous oxidation-xylenol orange (FOX) assay, and this activity is blocked by thiol alkylating reagents.

Conclusion

Thus, this hypothetical protein was assigned to the AhpD-like protein family with peroxidase-related activity. The functional relationship of specific oligomeric structures of AhpD-like structural family is discussed.