Kajsa G. V. Sigfridsson

Hydride binding to the active site of [FeFe]-hydrogenase.

[FeFe]-hydrogenase from green algae (HydA1) is the most efficient hydrogen (H2) producing enzyme in nature and of prime interest for (bio)technology. Its active site is a unique six-iron center (H-cluster) composed of a cubane cluster, [4Fe4S]H, cysteine-linked to a diiron unit, [2Fe]H, which carries unusual carbon monoxide (CO) and cyanide ligands and a bridging azadithiolate group. We have probed the molecular and electronic configurations of the H-cluster in functional oxidized, reduced, and super-reduced or CO-inhibited HydA1 protein, in particular searching for intermediates with iron-hydride bonds. Site-selective X-ray absorption and emission spectroscopy were used to distinguish between low- and high-spin iron sites in the two subcomplexes of the H-cluster. The experimental methods and spectral simulations were calibrated using synthetic model complexes with ligand variations and bound hydride species. Distinct X-ray spectroscopic signatures of electronic excitation or decay transitions in [4Fe4S]H and [2Fe]H were obtained, which were quantitatively reproduced by density functional theory calculations, thereby leading to specific H-cluster model structures. We show that iron-hydride bonds are absent in the reduced state, whereas only in the super-reduced state, ligand rotation facilitates hydride binding presumably to the Fe-Fe bridging position at [2Fe]H. These results are in agreement with a catalytic cycle involving three main intermediates and at least two protonation and electron transfer steps prior to the H2 formation chemistry in [FeFe]-hydrogenases.

Electronic and molecular structures of the active-site H-cluster in [FeFe]-hydrogenase determined by site-selective X-ray spectroscopy and quantum chemical calculations

The [FeFe]-hydrogenase (HydA1) from green algae is the minimal enzyme for efficient biological hydrogen (H2) production. Its active-site six-iron center (H-cluster) consists of a cubane, [4Fe4S]H, cysteine-linked to a diiron site, [2Fe]H. We utilized the spin-polarization of the iron Kβ X-ray fluorescence emission to perform site-selective X-ray absorption experiments for spectral discrimination of the two sub-complexes. For the H-cluster in reduced HydA1 protein, XANES and EXAFS spectra, Kβ emission lines (3p → 1s transitions), and core-to-valence (pre-edge) absorption (1s → 3d) and valence-to-core (Kβ2,5) emission (3d → 1s) spectra were obtained, individually for [4Fe4S]H and [2Fe]H. Iron–ligand bond lengths and intermetal distances in [2Fe]H and [4Fe4S]H were resolved, as well as fine structure in the high-spin iron containing cubane. Density functional theory calculations reproduced the X-ray spectral features and assigned the molecular orbital configurations, emphasizing the asymmetric d-level degeneracy of the proximal (Fep) and distal (Fed) low-spin irons in [2Fe]H in the non-paramagnetic state. This yielded a specific model structure of the H-cluster with a bridging carbon monoxide ligand and an apical open coordination site at Fed in [2Fe]H. The small HOMO–LUMO gap (∼0.3 eV) enables oxidation and reduction of the active site at similar potentials for reversible H2 turnover by HydA1, the LUMO spread over [4Fe4S]H supports its role as an electron transfer relay, and Fed carrying the HOMO is prepared for transient hydride binding. These features and the accessibility of Fed from the bulk phase can account for regio-specific redox transitions as well as H2-formation and O2-inhibition at the H-cluster. We provide a conceptual and experimental framework for site-selective studies on catalytic mechanisms in inhomogeneous materials.

Rapid X-ray Photoreduction of Dimetal-Oxygen Cofactors in Ribonucleotide Reductase

Background: Typical FeFe and MnFe cofactors bind to numerous enzymes such as ribonucleotide reductases. Crystallographic data suggest x-ray photoreduction (XPR) effects. Results: Rapid XPR-induced cofactor changes were monitored using time-resolved x-ray absorption spectroscopy. Conclusion: The XPR-induced cofactor states differ significantly from the native configurations, but comply with crystallographic structures. Significance: Structure determination for high-valent dimetal-oxygen cofactors requires free electron-laser protein crystallography combined with x-ray spectroscopy. Prototypic dinuclear metal cofactors with varying metallation constitute a class of O2-activating catalysts in numerous enzymes such as ribonucleotide reductase. Reliable structures are required to unravel the reaction mechanisms. However, protein crystallography data may be compromised by x-ray photoreduction (XRP). We studied XPR of Fe(III)Fe(III) and Mn(III)Fe(III) sites in the R2 subunit of Chlamydia trachomatis ribonucleotide reductase using x-ray absorption spectroscopy. Rapid and biphasic x-ray photoreduction kinetics at 20 and 80 K for both cofactor types suggested sequential formation of (III,II) and (II,II) species and similar redox potentials of iron and manganese sites. Comparing with typical x-ray doses in crystallography implies that (II,II) states are reached in <1 s in such studies. First-sphere metal coordination and metal-metal distances differed after chemical reduction at room temperature and after XPR at cryogenic temperatures, as corroborated by model structures from density functional theory calculations. The inter-metal distances in the XPR-induced (II,II) states, however, are similar to R2 crystal structures. Therefore, crystal data of initially oxidized R2-type proteins mostly contain photoreduced (II,II) cofactors, which deviate from the native structures functional in O2 activation, explaining observed variable metal ligation motifs. This situation may be remedied by novel femtosecond free electron-laser protein crystallography techniques.

Identification of a bis-molybdopterin intermediate in molybdenum cofactor biosynthesis in Escherichia coli

Background: Some molybdoenzymes in prokaryotes contain the bis-molybdopterin guanine dinucleotide cofactor. Results: The bis-Mo-MPT cofactor is a novel intermediate in Moco biosynthesis in E. coli. Conclusion: Bis-MGD formed by MobA is fully functional and restores the catalytic activity in apoTorA. Significance: Bis-Mo-MPT assembles spontaneously on MobA prior to forming bis-MGD. The molybdenum cofactor is an important cofactor, and its biosynthesis is essential for many organisms, including humans. Its basic form comprises a single molybdopterin (MPT) unit, which binds a molybdenum ion bearing three oxygen ligands via a dithiolene function, thus forming Mo-MPT. In bacteria, this form is modified to form the bis-MPT guanine dinucleotide cofactor with two MPT units coordinated at one molybdenum atom, which additionally contains GMPs bound to the terminal phosphate group of the MPTs (bis-MGD). The MobA protein catalyzes the nucleotide addition to MPT, but the mechanism of the biosynthesis of the bis-MGD cofactor has remained enigmatic. We have established an in vitro system for studying bis-MGD assembly using purified compounds. Quantification of the MPT/molybdenum and molybdenum/phosphorus ratios, time-dependent assays for MPT and MGD detection, and determination of the numbers and lengths of Mo–S and Mo–O bonds by X-ray absorption spectroscopy enabled identification of a novel bis-Mo-MPT intermediate on MobA prior to nucleotide attachment. The addition of Mg-GTP to MobA loaded with bis-Mo-MPT resulted in formation and release of the final bis-MGD product. This cofactor was fully functional and reconstituted the catalytic activity of apo-TMAO reductase (TorA). We propose a reaction sequence for bis-MGD formation, which involves 1) the formation of bis-Mo-MPT, 2) the addition of two GMP units to form bis-MGD on MobA, and 3) the release and transfer of the mature cofactor to the target protein TorA, in a reaction that is supported by the specific chaperone TorD, resulting in an active molybdoenzyme.

Improved arsenic(III) adsorption by Al2O3 nanoparticles and H2O2: Evidence of oxidation to arsenic(V) from X-ray absorption spectroscopy

We have investigated the oxidation of inorganic As(III) with H2O2 catalysed by Al2O3, using X-ray absorption near-edge structure and extended X-ray absorption fine structure spectroscopy. The effects of different reaction conditions (pH, time and initial H2O2 concentration) were also studied as were the kinetics of the oxidation reaction. We demonstrated that As(III) was oxidized to As(V) in the presence of H2O2 and Al2O3. Furthermore, all arsenic species found on the Al2O3 surface were in the As(V) state. The presence of both Al2O3 and H2O2 was necessary for oxidation of As(III) to take place within the period of time studied. The oxidation kinetics indicate a mechanism where reversible As(III) binding to the alumina surface is followed by irreversible oxidation by H2O2 leading to strongly bound As(V). Results from this study indicate that there is a surface-catalysed oxidation of As(III) on Al2O3 by H2O2, a reaction that can take place in nature and can be of help in the development of novel treatment systems for As(III) removal.

Effect of Exchange of the Cysteine Molybdenum Ligand with Selenocysteine on the Structure and Function of the Active Site in Human Sulfite Oxidase

Sulfite oxidase (SO) is an essential molybdoenzyme for humans, catalyzing the final step in the degradation of sulfur-containing amino acids and lipids, which is the oxidation of sulfite to sulfate. The catalytic site of SO consists of a molybdenum ion bound to the dithiolene sulfurs of one molybdopterin (MPT) molecule, carrying two oxygen ligands, and is further coordinated by the thiol sulfur of a conserved cysteine residue. We have exchanged four non-active site cysteines in the molybdenum cofactor (Moco) binding domain of human SO (SOMD) with serine using site-directed mutagenesis. This facilitated the specific replacement of the active site Cys207 with selenocysteine during protein expression in Escherichia coli. The sulfite oxidizing activity (kcat/KM) of SeSOMD4Ser was increased at least 1.5-fold, and the pH optimum was shifted to a more acidic value compared to those of SOMD4Ser and SOMD4Cys(wt). X-ray absorption spectroscopy revealed a Mo(VI)-Se bond length of 2.51 Å, likely caused by the specific binding of Sec207 to the molybdenum, and otherwise rather similar square-pyramidal S/Se(Cys)O2Mo(VI)S2(MPT) site structures in the three constructs. The low-pH form of the Mo(V) electron paramagnetic resonance (EPR) signal of SeSOMD4Ser was altered compared to those of SOMD4Ser and SOMD4Cys(wt), with g1 in particular shifted to a lower magnetic field, due to the Se ligation at the molybdenum. In contrast, the Mo(V) EPR signal of the high-pH form was unchanged. The substantially stronger effect of substituting selenocysteine for cysteine at low pH as compared to high pH is most likely due to the decreased covalency of the Mo-Se bond.

Structural differences of oxidized iron-sulfur and nickel-iron cofactors in O2-tolerant and O2-sensitive hydrogenases studied by X-ray absorption spectroscopy.

The class of [NiFe]-hydrogenases comprises oxygen-sensitive periplasmic (PH) and oxygen-tolerant membrane-bound (MBH) enzymes. For three PHs and four MBHs from six bacterial species, structural features of the nickel-iron active site of hydrogen turnover and of the iron-sulfur clusters functioning in electron transfer were determined using X-ray absorption spectroscopy (XAS). Fe-XAS indicated surplus oxidized iron and a lower number of ~2.7 Å Fe-Fe distances plus additional shorter and longer distances in the oxidized MBHs compared to the oxidized PHs. This supported a double-oxidized and modified proximal FeS cluster in all MBHs with an apparent trimer-plus-monomer arrangement of its four iron atoms, in agreement with crystal data showing a [4Fe3S] cluster instead of a [4Fe4S] cubane as in the PHs. Ni-XAS indicated coordination of the nickel by the thiol group sulfurs of four conserved cysteines and at least one iron-oxygen bond in both MBH and PH proteins. Structural differences of the oxidized inactive [NiFe] cofactor of MBHs in the Ni-B state compared to PHs in the Ni-A state included a ~0.05 Å longer Ni-O bond, a two times larger spread of the Ni-S bond lengths, and a ~0.1 Å shorter Ni-Fe distance. The modified proximal [4Fe3S] cluster, weaker binding of the Ni-Fe bridging oxygen species, and an altered localization of reduced oxygen species at the active site may each contribute to O2 tolerance.

High performance emission spectrometer at Balder/MAX IV beamline

The emission spectrometer at Balder/MAX IV beamline is presented. Its unique features are described. Comparison is given with other types of curved crystals analyzers.