Structural details of the OxyR peroxide-sensing mechanism

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 20, 2015, Pages 6443-6448

  Jo, Inseong ^a   Chung, In Young ^b   Bae, Hee Won ^b   Kim, Jin Sik ^a   Song, Saemee ^a   Cho, You Hee ^b   Ha, Nam Chul ^a  

^a Seoul National University   (South Korea)

^b CHA University   (South Korea)

Author keywords

Conformational change; Hydrogen peroxide; OxyR; Reaction mechanism; Transcription regulator

Indexed keywords

CYSTEINE; HYDROGEN PEROXIDE; MUTANT PROTEIN; PROTEIN OXYR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; OXYR PROTEIN, PSEUDOMONAS AERUGINOSA; PROTEIN BINDING; TRANSACTIVATOR PROTEIN;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DIMERIZATION; HYDROGEN BOND; HYDROXYLATION; MOLECULAR MODEL; NONHUMAN; OXIDATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTEIN STRUCTURE; PSEUDOMONAS AERUGINOSA; X RAY DIFFRACTION; CHEMICAL STRUCTURE; CHEMISTRY; CRYSTALLIZATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; OXIDATION REDUCTION REACTION; PHYSIOLOGY; POLYMERASE CHAIN REACTION; SITE DIRECTED MUTAGENESIS;

BACTERIA (MICROORGANISMS); PSEUDOMONAS AERUGINOSA;

BINDING SITES; CRYSTALLIZATION; GENE EXPRESSION REGULATION, BACTERIAL; HYDROGEN PEROXIDE; MODELS, MOLECULAR; MOLECULAR STRUCTURE; MUTAGENESIS, SITE-DIRECTED; OXIDATION-REDUCTION; POLYMERASE CHAIN REACTION; PROTEIN BINDING; PROTEIN CONFORMATION; TRANS-ACTIVATORS; X-RAY DIFFRACTION;

EID: 84929430296     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1424495112     Document Type: Article

References (25)

1. Antelmann H, Helmann JD (2011) Thiol-based redox switches and gene regulation. Antioxid Redox Signal 14(6):1049-1063.
2. Imlay JA (2008) Cellular defenses against superoxide and hydrogen peroxide. Annu Rev Biochem 77:755-776.
3. Storz G, Tartaglia LA, Farr SB, Ames BN (1990) Bacterial defenses against oxidative stress. Trends Genet 6(11):363-368.
4. Aslund F, Zheng M, Beckwith J, Storz G (1999) Regulation of the OxyR transcription factor by hydrogen peroxide and the cellular thiol-disulfide status. Proc Natl Acad Sci USA 96(11):6161-6165.
5. Schell MA (1993) Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47:597-626.
6. Choi H, et al. (2001) Structural basis of the redox switch in the OxyR transcription factor. Cell 105(1):103-113.
7. Lee C, et al. (2004) Redox regulation of OxyR requires specific disulfide bond formation involving a rapid kinetic reaction path. Nat Struct Mol Biol 11(12):1179-1185.
8. Toledano MB, et al. (1994) Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: A mechanism for differential promoter selection. Cell 78(5):897-909.
9. Panmanee W, Hassett DJ (2009) Differential roles of OxyR-controlled antioxidant enzymes alkyl hydroperoxide reductase (AhpCF) and catalase (KatB) in the protection of Pseudomonas aeruginosa against hydrogen peroxide in biofilm vs. planktonic culture. FEMS Microbiol Lett 295(2):238-244.
10. Hishinuma S, Yuki M, Fujimura M, Fukumori F (2006) OxyR regulated the expression of two major catalases, KatA and KatB, along with peroxiredoxin, AhpC in Pseudomonas putida. Environ Microbiol 8(12):2115-2124.
11. Bae HW, Cho YH (2012) Mutational analysis of Pseudomonas aeruginosa OxyR to define the regions required for peroxide resistance and acute virulence. Res Microbiol 163(1):55-63.
12. Kullik I, Stevens J, Toledano MB, Storz G (1995) Mutational analysis of the redox-sensitive transcriptional regulator OxyR: Regions important for DNA binding and multimerization. J Bacteriol 177(5):1285-1291.
13. Dubbs JM, Mongkolsuk S (2012) Peroxide-sensing transcriptional regulators in bacteria. J Bacteriol 194(20):5495-5503.
14. Nakamura T, et al. (2010) Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide. J Biochem 147(1):109-115.
15. Sainsbury S, et al. (2010) The structure of a reduced form of OxyR from Neisseria meningitidis. BMC Struct Biol 10:10.
16. Svintradze DV, Peterson DL, Collazo-Santiago EA, Lewis JP, Wright HT (2013) Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis. Acta Crystallogr D Biol Crystallogr 69(Pt 10):2091-2103.
17. Saha S, Das KP (2013) Structure and interactions in alpha-crystallin probed through thiol group reactivity. Adv Biol Chem 3(5):427-439.
18. Hall A, Parsonage D, Poole LB, Karplus PA (2010) Structural evidence that peroxiredoxin catalytic power is based on transition-state stabilization. J Mol Biol 402(1):194-209.
19. Ferrer-Sueta G, et al. (2011) Factors affecting protein thiol reactivity and specificity in peroxide reduction. Chem Res Toxicol 24(4):434-450.
20. Heo YJ, et al. (2010) The major catalase gene (katA) of Pseudomonas aeruginosa PA14 is under both positive and negative control of the global transactivator OxyR in response to hydrogen peroxide. J Bacteriol 192(2):381-390.
21. Landt O, Grunert HP, Hahn U (1990) A general method for rapid site-directed mutagenesis using the polymerase chain reaction. Gene 96(1):125-128.
22. Winn MD, et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67(Pt 4):235-242.
23. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2126-2132.
24. DiMaio F, et al. (2013) Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nat Methods 10(11):1102-1104.
25. Ellman GL, Courtney KD, Andres V, Jr, Feather-Stone RM (1961) A new and rapid colorimetric determination of acetylcholinesterase activity. Biochem Pharmacol 7:88-95.