title: Crystal structure of alkyl hydroperoxidase D like protein PA0269 from Pseudomonas aeruginosa: homology of the AhpD-like structural family.
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 H(2)O(2) as tested using a ferrous oxidation-xylenol orange (FOX) assay, and this activity is blocked by thiol alkylating reagents.
  
  
  CONCLUSIONS
  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.
authors: Campbell Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada.
authors: Teresa E
authors: TE
authors: Clarke
authors: Vladimir
authors: V
authors: Romanov
authors: Yuri N
authors: YN
authors: Chirgadze
authors: Chananat
authors: C
authors: Klomsiri
authors: Gera
authors: G
authors: Kisselman
authors: Jean
authors: J
authors: Wu-Brown
authors: Leslie B
authors: LB
authors: Poole
authors: Emil F
authors: EF
authors: Pai
authors: Nickolay Y
authors: NY
authors: Chirgadze
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W615-9
references: 15215462
references: J Biol Chem. 2000 Jun 23;275(25):18801-9
references: 10766746
references: Methods Enzymol. 1997;276:307-26
references: 27754618
references: CSH Protoc. 2007 Jul 01;2007:pdb.top17
references: 21357135
references: Brief Bioinform. 2001 May;2(2):195-7
references: 11465736
references: Structure. 2008 Dec 10;16(12):1755-63
references: 19081051
references: Science. 2002 Feb 8;295(5557):1073-7
references: 11799204
references: Biochemistry. 1997 Oct 28;36(43):13349-56
references: 9341227
references: Methods Mol Biol. 2007;364:215-30
references: 17172768
references: Protein Sci. 2006 May;15(5):1187-92
references: 16597838
references: Mol Cell. 1998 May;1(6):795-805
references: 9660963
references: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2256-68
references: 15572779
references: Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3
references: 15299374
references: Arch Biochem Biophys. 2004 Jul 1;427(1):41-7
references: 15178486
references: J Biol Chem. 2002 May 31;277(22):20033-40
references: 11914371
references: J Mol Biol. 1977 May 25;112(3):535-42
references: 875032
references: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references: 15572765
references: J Mol Biol. 1993 Sep 5;233(1):123-38
references: 8377180
references: J Biol Chem. 2003 Aug 8;278(32):29502-8
references: 12761216