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• High (valent) on O₂: Ribonucleotide Reductase and Methane Monooxygenase

  2023. Juliane John.

  Avhandling (Dok)

  Macromolecular X-ray crystallography (MX) is a powerful method to investigate protein structures. However, proteins with redox-active centres and radicals are very susceptible to photoreduction. It is therefore challenging to acquire structural details of redox-active centres in defined oxidation states or protein radicals using synchrotron radiation. Serial femtosecond crystallography (SFX) using X-ray free electron laser (XFEL) radiation mitigates this problem. XFELs produce intense pulses of femtosecond length that give rise to diffraction before photoinduced movement can occur in the illuminated protein. Additionally, SFX allows experiments at room temperature and induction of reactions in crystallo. 

  In this thesis two different redox-active enzyme systems were investigated with MX and SFX. The first part examines ribonucleotide reductase (RNR). RNR is the only known enzyme to synthesize de novo deoxyribonucleotides, the building blocks of DNA. Class I RNR consists of a small subunit R2 and a large subunit R1. R2 generates a radical in an oxygen dependent way and delivers it to R1 for ribonucleotide reduction. After catalysis the radical is transferred back to R2 until further use. Class I RNR is divided in five subclasses, mostly based on their mechanism of radical generation. In Paper I class Ib R2 is investigated. R2b binds two manganese ions that react with superoxide to produce a radical. The superoxide is provided by a small flavoprotein, NrdI, bound to R2. When exposed to molecular oxygen, reduced NrdI generates superoxide that is transferred to the R2 active site. Here two SFX structures of reduced and oxidized NrdI in complex with R2 are presented and it is suggested how the binding and NrdI oxidation state could influence the superoxide production. In Paper II the SFX structure of a R2e protein radical is presented. Class Ie R2 contains a metal-free active site. The comparison of the radical structure with a ground state structure highlights the changes induced by radical formation. A mechanism for the initiation of the radical transfer to R1 is proposed based on the structural details observed. In Paper III light is shed on a new variant of R2e. Three of the typically conserved active site residues are mutated in R2e; from three glutamates to valine, proline and lysine (VPK) or to glutamine, serine and lysine (QSK). Other publications, including Paper II, describe the VPK mutation but as of now the QSK variant has not been examined. Here, crystal structures of a R2e QSK protein are shown. A tyrosine close to the active site is post-translationally modified to a dihydroxyphenylalanine (DOPA). The amount of modified protein is shown to scale with the coexpression of other proteins of the RNR operon. 

  The second redox-active enzyme investigated is soluble methane monooxygenase (sMMO). sMMO oxidizes methane to methanol and is produced by methanotrophs; bacteria that use methane as their sole carbon source. Methane is a potent greenhouse gas and can be found in ever increasing concentrations in the atmosphere due to human activities; sMMO is thus a compelling target for biotechnological development. Paper IV presents SFX structures of the catalytic subunit MMOH in complex with its small regulatory subunit MMOB in the oxidized and reduced resting state. It is also demonstrated that the complex can undergo the catalytic cycle in crystallo, allowing investigation of reaction cycle intermediates in the future. 

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• Structure of a ribonucleotide reductase R2 protein radical

  2023. Hugo Lebrette (et al.). Science 382 (6666), 109-113

  Artikel

  Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). We present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O–O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins. 

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• Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography

  2022. Juliane John (et al.). eLIFE 11

  Artikel

  Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b–NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.

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• Versatile microporous polymer-based supports for serial macromolecular crystallography

  2021. Isabelle Martiel (et al.). Acta Crystallographica Section D 77, 1153-1167

  Artikel

  Serial data collection has emerged as a major tool for data collection at state-of-the-art light sources, such as microfocus beamlines at synchrotrons and X-ray free-electron lasers. Challenging targets, characterized by small crystal sizes, weak diffraction and stringent dose limits, benefit most from these methods. Here, the use of a thin support made of a polymer-based membrane for performing serial data collection or screening experiments is demonstrated. It is shown that these supports are suitable for a wide range of protein crystals suspended in liquids. The supports have also proved to be applicable to challenging cases such as membrane proteins growing in the sponge phase. The sample-deposition method is simple and robust, as well as flexible and adaptable to a variety of cases. It results in an optimally thin specimen providing low background while maintaining minute amounts of mother liquor around the crystals. The 2 × 2 mm area enables the deposition of up to several microlitres of liquid. Imaging and visualization of the crystals are straightforward on the highly transparent membrane. Thanks to their affordable fabrication, these supports have the potential to become an attractive option for serial experiments at synchrotrons and free-electron lasers.

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• High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States

  2020. Vivek Srinivas (et al.). Journal of the American Chemical Society 142 (33), 14249-14266

  Artikel

  Soluble methane monooxygenase (sMMO)is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O-2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the <= 35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 angstrom resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. This study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.

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