Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase. Issue 23 (20th November 2016)

• Record Type: Journal Article
• Authors: Romão, Célia V.; Vicente, João B.; Borges, Patrícia T.; Victor, Bruno L.; Lamosa, Pedro; Silva, Elísio; Pereira, Luís; Bandeiras, Tiago M.; Soares, Cláudio M.; Carrondo, Maria A.; Turner, David; Teixeira, Miguel; Frazão, Carlos
• Is Part Of: Journal of molecular biology. Volume 428:Issue 23(2016:Nov. 20)
• Page Start: 4686
• Page End: 4707
• Publication Date: 2016-11-20
• Subjects: NO nitric oxide -- Hmp flavohaemoglobin -- FlRd flavorubredoxin -- FDP flavodiiron protein -- FMN flavin mononucleotide -- Rd rubredoxin -- MD molecular dynamics -- SAXS small-angle X-ray scattering -- a.u. asymmetric unit -- SAS solvent-accessible surface -- a.d.p. atomic displacement parameter -- μ-OHˉ μ-hydroxo -- PEG polyethylene glycol -- ESRF European Synchrotron Research Facility -- DLS Diamond Light Source -- TLS translation, libration, and screw -- NOESY Nuclear Overhauser enhancement spectroscopy -- TOCSY total correlation spectra -- HSQC heteronuclear single quantum coherence -- SPC single point charge; flavorubredoxin -- flavodiiron protein -- NorV -- diiron center -- nitric oxide; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2016.10.008
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: Flavodiiron proteins (FDPs) are present in organisms from all domains of life and have been described so far to be involved in the detoxification of oxygen or nitric oxide (NO), acting as O2 and/or NO reductases. The Escherichia coli FDP, named flavorubredoxin (FlRd), is the most extensively studied FDP. Biochemical and in vivo studies revealed that FlRd is involved in NO detoxification as part of the bacterial defense mechanisms against reactive nitrogen species. E. coli FlRd has a clear preference for NO as a substrate in vitro, exhibiting a very low reactivity toward O2 . To contribute to the understanding of the structural features defining this substrate selectivity, we determined the crystallographic structure of E. coli FlRd, both in the isolated and reduced states. The overall tetrameric structure revealed a highly conserved flavodiiron core domain, with a metallo-β-lactamase-like domain containing a diiron center, and a flavodoxin domain with a flavin mononucleotide cofactor. The metal center in the oxidized state has a μ-hydroxo bridge coordinating the two irons, while in the reduced state, this moiety is not detected. Since only the flavodiiron domain was observed in these crystal structures, the structure of the rubredoxin domain was determined by NMR. Tunnels for the substrates were identified, and through molecular dynamics simulations, no differences for O2 or NO permeation were found. The present data represent the first structure for a NO-selective FDP. Graphical Abstract: Highlights: Crystal structure of the NO selective Escherichia coli flavodiiron protein Oxidized and reduced protein crystals reveal structural differences at the diiron site. Protein tunnels for substrates/products were identified. Chain of aromatic residues connects the diiron site to the protein surface.