Evolution of Bacterial and Archaeal Multicomponent Monooxygenases

Notomista, Eugenio; Lahm, Armin; Donato, Alberto Di; Tramontano, Anna

doi:10.1007/s00239-002-2414-1

Cited by 121 publications

(127 citation statements)

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“…Such structural differences are not surprising given the poor sequence conservation for this subunit among the different BMM family members. The function of this subunit, which is absent in some BMMs like alkene monooxygenases, is unclear (2,3,11).…”

Section: Phh Global Foldmentioning

confidence: 99%

“…TMOs and SsoMOs differ slightly since they utilize an additional, Rieske protein to assist with electron transfer between the reductase and hydroxylase components (2,3). The active sites in the resting states of the methane (MMOH) and toluene/o-xylene (ToMOH) monooxygenase hydroxylases contain a diiron(III) center coordinated by four glutamate and two histidine ligands from a four-helix bundle composed of helices B, C, E, and F of the protein α-subunit (8,9).…”

mentioning

confidence: 99%

“…A diiron(IV) intermediate has not been detected in any other BMM hydroxylase, but recent work has identified oxygenated diiron(III) species capable of oxidizing aromatic substrates (15). 2 , 3 1 Abbreviations: ACP, acyl carrier protein; AMO, alkene monooxygenase; APS, Advanced Photon Source; BMM, bacterial multicomponent monooxygenase; C2,3O, catechol 2,3-dioxygenase; PH, phenol hydroxylase; PHH, phenol hydroxylase hydroxylase component; PHM, phenol hydroxylase regulatory protein; PHP, phenol hydroxylase reductase; MMOB, methane monooxygenase regulatory protein; MMOH, methane monooxygenase hydroxylase; MMOR, methane monooxygenase reductase; rmsd, root-meansquare deviation; sMMO, soluble methane monooxygenase; SsoMO, hyperthermophilic toluene monooxygenase; SSRL, Stanford Synchrotron Radiation Laboratory; T4MO, toluene 4-monooxygenase; T4MOD, toluene 4-monooxygenase regulatory protein; THFMO, tetrahydrofuran monooxygenase; TMO, toluene monooxygenase; TOM, toluene o-monooxygenase; ToMO, toluene/o-xylene monooxygenase; ToMOD, toluene/o-xylene monooxygenase regulatory protein; ToMOH, toluene/o-xylene monooxygenase hydroxylase. Comparisons between the MMOH and ToMOH structures have provided insight into how the protein scaffold may tune the reactivity and substrate specificity of the diiron center by controlling the access of small molecules to the active site pocket.…”

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confidence: 99%

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X-ray Structure of a Hydroxylase−Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase^,

et al. 2006

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Phenol hydroxylase (PH) belongs to a family of bacterial multicomponent monooxygenases (BMMs) with carboxylate-bridged diiron active sites. Included are toluene/o-xylene (ToMO) and soluble methane (sMMO) monooxygenase. PH hydroxylates aromatic compounds, but unlike sMMO, it cannot oxidize alkanes despite having a similar dinuclear iron active site. Important for activity is formation of a complex between the hydroxylase and a regulatory protein component. To address how structural features of BMM hydroxylases and their component complexes may facilitate the catalytic mechanism and choice of substrate, we determined X-ray structures of native and SeMet forms of the PH hydroxylase (PHH) in complex with its regulatory protein (PHM) to 2.3 Å resolution. PHM binds in a canyon on one side of the (αβγ) 2 PHH dimer, contacting α-subunit helices A, E, and F ∼12 Å above the diiron core. The structure of the dinuclear iron center in PHH resembles that of mixed-valent MMOH, suggesting an Fe(II)Fe(III) oxidation state. Helix E, which comprises part of the iron-coordinating four-helix bundle, has more π-helical character than analogous E helices in MMOH and ToMOH lacking a bound regulatory protein. Consequently, conserved active site Thr and Asn residues translocate to the protein surface, and an ∼6 Å pore opens through the four-helix bundle. Of likely functional significance is a specific hydrogen bond formed between this Asn residue and a conserved Ser side chain on PHM. The PHM protein covers a putative docking site on PHH for the PH reductase, which transfers electrons to the PHH diiron center prior to O 2 activation, † This research was supported by National Institute of General Medical Sciences Grant GM32134 (S.J.L.) and the Italian Ministry of SUPPORTING INFORMATION AVAILABLE BMM hydroxylase and regulatory protein structures and their electrostatic surfaces (Figures S1 and S2), packing of the β-subunit Nterminus and a γ-subunit from an adjacent molecule in the PHH canyon ( Figure S3), comparison of known regulatory protein structures ( Figure S4), sequence alignments of the different regulatory proteins ( Figure S5), models of the PHH diiron center in electron density maps ( Figure S6), comparison of the hydroxylase zinc-binding sequences ( Figure S7), and electron density maps around helix F ( Figure S8). This material is available free of charge via the Internet at http://pubs.acs.org. NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2007 March 21. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscriptsuggesting that the regulatory component may function to block undesired reduction of oxygenated intermediates during the catalytic cycle. A series of hydrophobic cavities through the PHH α-subunit, analogous to those in MMOH, may facilitate movement of the substrate to and/or product from the active site pocket. Comparisons between the ToMOH and PHH structures provide insights into their substrate regiospecificities.Bacterial multicomponent monooxygenases...

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Section: Phh Global Foldmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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X-ray Structure of a Hydroxylase−Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase^,

et al. 2006

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“…Four characterized subclasses of multicomponent monooxygenases have been defined (2,3). These are soluble methane monooxygenases (sMMOs), four-component alkene/arene monooxygenases or toluene monooxygenases (TMOs), three-component phenol hydroxylases (PHs), and ␣␤ alkene monoxygenases (AMOs), of which all are believed to have evolved from a common ancestor.…”

mentioning

confidence: 99%

Crystal Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase from Pseudomonas stutzeri OX1

Sazinsky

Bard²,

Donato

et al. 2004

Journal of Biological Chemistry

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The four-component toluene/o-xylene monooxygenase (ToMO) from Pseudomonas stutzeri OX1 is capable of oxidizing arenes, alkenes, and haloalkanes at a carboxylate-bridged diiron center similar to that of soluble methane monooxygenase (sMMO). The remarkable variety of substrates accommodated by ToMO invites applications ranging from bioremediation to the regioand enantiospecific oxidation of hydrocarbons on an industrial scale. We report here the crystal structures of the ToMO hydroxylase (ToMOH), azido ToMOH, and ToMOH containing the product analogue 4-bromophenol to 2.3 Å or greater resolution. The catalytic diiron(III) core resembles that of the sMMO hydroxylase, but aspects of the ␣ 2 ␤ 2 ␥ 2 tertiary structure are notably different. Of particular interest is a 6 -10 Å-wide channel of ϳ35 Å in length extending from the active site to the protein surface. The presence of three bromophenol molecules in this space confirms this route as a pathway for substrate entrance and product egress. An analysis of the ToMOH active site cavity offers insights into the different substrate specificities of multicomponent monooxygenases and explains the behavior of mutant forms of homologous enzymes described in the literature.Bacterial multicomponent monooxygenases (BMMs) 1 comprise a family of carboxylate-bridged non-heme diiron enzymes capable of oxidizing a broad range of hydrocarbons including C 1 -C 8 alkanes, alkenes, and aromatics (1, 2). Four characterized subclasses of multicomponent monooxygenases have been defined (2, 3). These are soluble methane monooxygenases (sMMOs), four-component alkene/arene monooxygenases or toluene monooxygenases (TMOs), three-component phenol hydroxylases (PHs), and ␣␤ alkene monoxygenases (AMOs), of which all are believed to have evolved from a common ancestor. Bacteria containing multicomponent monooxygenases are capable of using specific hydrocarbon substrates as their primary source of carbon and energy (1, 2, 4). The remarkable range of substrate specificity exhibited by these enzymes endows these bacteria with the ability to bioremediate environmentally harmful substances such as trichloroethylene and petroleum spills (5, 6) and to regulate the global carbon cycle (4). BMMs can also perform regio-and stereospecific hydroxylations, making them useful for producing pure feedstocks for industrial synthesis (7). These enzyme systems, although highly homologous, have evolved different substrate specificities. Only soluble methane monooxygenase can activate the inert C-H bond of methane, which is one of the most difficult reactions to perform in nature (1), whereas the catalytic abilities of TMOs are limited to aromatics, alkenes, and some haloalkanes (2, 5).Substrate hydroxylation in BMMs occurs at a dioxygen-activated, carboxylate-bridged diiron center in the ␣-subunit of a ϳ220 -250 kDa hydroxylase component that is an (␣␤␥) 2 heterodimer or, in the case of one known AMO, an ␣␤ monomer (1-3, 8, 9). Sequence identity comparisons and spectroscopic studies suggest that the diiron centers of...

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“…The BMM members consist of short electron transport components. BMMs play a key role in global methane cycling and biodegradation of toxic compounds (Notomista et al, 2003). Thus, the full understanding of BMMs at biochemical levels will aid in solving related global environmental problems.…”

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confidence: 99%

Construction of Overexpression Vectors and Purification of the Oxygenase Component of Alkylphenol Hydroxylase of Pseudomonas alkylphenolia

Lee¹

2013

The Korean Journal of Microbiology

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Following construction of expression vectors in Escherichia coli, a new procedure involving two-step column purifications with a Fast Performance Liquid Chromatography System was developed for purification of the oxygenase component of alkylphenol hydroxylase of Pseudomonas alkylphenolia. From 50 g wet cake of recombinant E. coli BL21(DE3)(pJJPMO2) cells, 110 mg of pure protein in a heterodimeric form containing a stoichiometric amount of iron were obtained and it exhibited a specific activity of 147 nmole/min/mg.

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Evolution of Bacterial and Archaeal Multicomponent Monooxygenases

Cited by 121 publications

References 40 publications

X-ray Structure of a Hydroxylase−Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase^,

X-ray Structure of a Hydroxylase−Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase^,

Crystal Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase from Pseudomonas stutzeri OX1

Construction of Overexpression Vectors and Purification of the Oxygenase Component of Alkylphenol Hydroxylase of Pseudomonas alkylphenolia

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Evolution of Bacterial and Archaeal Multicomponent Monooxygenases

Cited by 121 publications

References 40 publications

X-ray Structure of a Hydroxylase−Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase,

X-ray Structure of a Hydroxylase−Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase,

Crystal Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase from Pseudomonas stutzeri OX1

Construction of Overexpression Vectors and Purification of the Oxygenase Component of Alkylphenol Hydroxylase of Pseudomonas alkylphenolia

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X-ray Structure of a Hydroxylase−Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase^,

X-ray Structure of a Hydroxylase−Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase^,