John H. Enemark

Molecular Basis of Sulfite Oxidase Deficiency from the Structure of Sulfite Oxidase

The molybdenum-containing enzyme sulfite oxidase catalyzes the conversion of sulfite to sulfate, the terminal step in the oxidative degradation of cysteine and methionine. Deficiency of this enzyme in humans usually leads to major neurological abnormalities and early death. The crystal structure of chicken liver sulfite oxidase at 1.9 A resolution reveals that each monomer of the dimeric enzyme consists of three domains. At the active site, the Mo is penta-coordinated by three sulfur ligands, one oxo group, and one water/hydroxo. A sulfate molecule adjacent to the Mo identifies the substrate binding pocket. Four variants associated with sulfite oxidase deficiency have been identified: two mutations are near the sulfate binding site, while the other mutations occur within the domain mediating dimerization.

Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers

This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at K(a) band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59±12Å. This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60Å, and analysis indicates that distance measurements up to 100Å are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.

The pH dependence of intramolecular electron transfer rates in sulfite oxidase at high and low anion concentrations

Abstract The individual rate constants for intramolecular electron transfer (IET) between the MoVIFeII and MoVFeIII forms of chicken liver sulfite oxidase (SO) have been determined at a variety of pH values, and at high and low anion concentrations. Large anions such as EDTA do not inhibit IET as dramatically as do small anions such as SO42– and Cl–, which suggests that specific anion binding at the sterically constrained Mo active site is necessary for IET inhibition to occur.IET may require that SO adopt a conformation in which the Mo and Fe centers are held in close proximity by electrostatic interactions between the predominantly positively charged Mo active site, and the negatively charged heme edge. Thus, small anions which can fit into the Mo active site will weaken this electrostatic attraction and disfavor IET. The rate constant for IET from FeII to MoVI decreases with increasing pH, both in the presence and absence of 50 mM SO42–. However, the rate constant for the reverse process exhibits no significant pH dependence in the absence of SO42–, and increases with pH in the presence of 50 mM SO42–. This behavior is consistent with a mechanism in which IET from MoV to FeIII is coupled to proton transfer from MoV–OH to OH–, and the reverse IET process is coupled to proton transfer from H2O to MoVI=O. At high concentrations of small anions, direct access of H2O or OH–to the Mo-OH will be blocked, which provides a second possible mechanism for inhibition of IET by such anions. Inhibition by anions is not strictly competitive, however, and Tyr322 may play an important intermediary role in transferring the proton when an anion blocks direct access of H2O or OH– to the Mo-OH. Competing H-bonding interactions of the Mo-OH moiety with Tyr322 and with the anion occupying the active site may also be responsible for the well-known equilibrium between two EPR-distinct forms of SO that is observed for the two-electron reduced enzyme.

Investigation of metal-dithiolate fold angle effects: implications for molybdenum and tungsten enzymes.

Gas-phase photoelectron spectroscopy and density functional theory have been used to investigate the interactions between the sulfur π-orbitals of arene dithiolates and high-valent transition metals as minimum molecular models of the active site features of pyranopterin Mo/W enzymes. The compounds (Tp*)MoO(bdt) (compound 1), Cp2Mo(bdt) (compound 2), and Cp2Ti(bdt) (compound 3) [where Tp* is hydrotris(3,5-dimethyl-1-pyrazolyl)borate, bdt is 1,2-benzenedithiolate, and Cp is η5- cyclopentadienyl] provide access to three different electronic configurations of the metal, formally d1, d2, and d0, respectively. The gas-phase photoelectron spectra show that ionizations from occupied metal and sulfur based valence orbitals are more clearly observed in compounds 2 and 3 than in compound 1. The observed ionization energies and characters compare very well with those calculated by density functional theory. A “dithiolate-folding-effect” involving an interaction of the metal in-plane and sulfur-π orbitals is proposed to be a factor in the electron transfer reactions that regenerate the active sites of molybdenum and tungsten enzymes.

The active sites of molybdenum- and tungsten-containing enzymes

Protein X-ray crystallography has revealed the structures of the active sites of several molybdenum- and tungsten-containing enzymes that catalyze formal hydroxylation and oxygen atom transfer reactions. Each molybdenum (or tungsten) atom is coordinated by one (or two) ene-dithiolate groups of a novel pterin (molybdopterin), and the active sites are further differentiated from one another by the number of terminal oxo and/or sulfido groups and by coordinated amino acid residues. These active-site structures have no precedent in the coordination chemistry of molybdenum and tungsten.

Effects of Interdomain Tether Length and Flexibility on the Kinetics of Intramolecular Electron Transfer in Human Sulfite Oxidase

Sulfite oxidase (SO) is a vitally important molybdenum enzyme that catalyzes the oxidation of toxic sulfite to sulfate. The proposed catalytic mechanism of vertebrate SO involves two intramolecular one-electron transfer (IET) steps from the molybdenum cofactor to the iron of the integral b-type heme and two intermolecular one-electron steps to exogenous cytochrome c. In the crystal structure of chicken SO [Kisker, C., et al. (1997) Cell 91, 973-983], which is highly homologous to human SO (HSO), the heme iron and molybdenum centers are separated by 32 A and the domains containing these centers are linked by a flexible polypeptide tether. Conformational changes that bring these two centers into greater proximity have been proposed [Feng, C., et al. (2003) Biochemistry 42, 5816-5821] to explain the relatively rapid IET kinetics, which are much faster than those theoretically predicted from the crystal structure. To explore the proposed role(s) of the tether in facilitating this conformational change, we altered both its length and flexibility in HSO by site-specific mutagenesis, and the reactivities of the resulting variants have been studied using laser flash photolysis and steady-state kinetics assays. Increasing the flexibility of the tether by mutating several conserved proline residues to alanines did not produce a discernible systematic trend in the kinetic parameters, although mutation of one residue (P105) to alanine produced a 3-fold decrease in the IET rate constant. Deletions of nonconserved amino acids in the 14-residue tether, thereby shortening its length, resulted in more drastically reduced IET rate constants. Thus, the deletion of five amino acid residues decreased IET by 70-fold, so that it was rate-limiting in the overall reaction. The steady-state kinetic parameters were also significantly affected by these mutations, with the P111A mutation causing a 5-fold increase in the sulfite K(m) value, perhaps reflecting a decrease in the ability to bind sulfite. The electron paramagnetic resonance spectra of these proline to alanine and deletion mutants are identical to those of wild-type HSO, indicating no significant change in the Mo active site geometry.

Effects of temperature and pressure on the molecular and electronic structure of N,N′-ethylenebis(salicylideneiminato)nitrosyliron, Fe(NO)(salen)

Abstract The crystal and molecular structures of the two magnetically distinct forms of Fe(NO)(salen), C 16 H 14 N 3 O 3 Fe, have been determined by single crystal X-ray diffraction at 23 °C and at −175 °C. The complex crystallizes in the orthorhombic space group Pna2 1 with 4 molecules per unit cell. The unit cell dimensions are a = 26.377(2), b = 8.598(5) and c = 6.951(5) A at 23 °C and a = 26.18(2), b = 8.52(1) and c = 6.783(6) A at −175 °C. Full-matrix least-squares refinement of the 23 °C structure based on the 840 reflections with F 2 o ⩾ 3σ(F 2 o ) gave a conventional R-factor of 0.038. The structure consists of discrete Fe(NO)(salen) molecules with tetragonal pyramidal coordination about the iron atom. The disordered nitrosyl group occupies the axial coordination site in a bent geometry (average FeNO angle 147°). Full-matrix least-squares refinement of the −175°C structure based on the 406 reflections with F 2 o ⩾ 2σ(F 2 o ) gave a conventional R-factor of 0.087. This form of Fe(NO)(salen) also exhibits tetragonal pyramidal coordination geometry with a bent disordered nitrosyl group in the apical position. Marginally significant structural changes are observed: 1) the FeNO angle is 127°; 2) the Fe atom is 0.1 A closer to the mean coordination plane of the salen ligand are more nearly coplanar. These structural changes are consistent with a spin state of Fe(NO)(salen) from S = 3 2 to S = 1 2 upon cooling. The significant differences in th conformations of the salen ligand at the two temperatures are attributed to crystal packing. The infrared spectra of Fe(NO)(salen) at room temperature for various pressures ranging from ambient pressure up to 37 kbar are reported. The spectra suggest that Fe(NO)(salen) is converted to the S = 1 2 state at high pressure.

Elucidating the catalytic mechanism of sulfite oxidizing enzymes using structural, spectroscopic, and kinetic analyses.

Sulfite oxidizing enzymes (SOEs) are molybdenum cofactor-dependent enzymes that are found in plants, animals, and bacteria. Sulfite oxidase (SO) is found in animals and plants, while sulfite dehydrogenase (SDH) is found in bacteria. In animals, SO catalyzes the oxidation of toxic sulfite to sulfate as the final step in the catabolism of the sulfur-containing amino acids, methionine and cysteine. In humans, sulfite oxidase deficiency is an inherited recessive disorder that produces severe neonatal neurological problems that lead to early death. Plant SO (PSO) also plays an important role in sulfite detoxification and in addition serves as an intermediate enzyme in the assimilatory reduction of sulfate. In vertebrates, the proposed catalytic mechanism of SO involves two intramolecular one-electron transfer (IET) steps from the molybdenum cofactor to the iron of the integral b-type heme. A similar mechanism is proposed for SDH, involving its molybdenum cofactor and c-type heme. However, PSO, which lacks an integral heme cofactor, uses molecular oxygen as its electron acceptor. Here we review recent results for SOEs from kinetic measurements, computational studies, electron paramagnetic resonance (EPR) spectroscopy, electrochemical measurements, and site-directed mutagenesis on active site residues of SOEs and of the flexible polypepetide tether that connects the heme and molybdenum domains of human SO. Rapid kinetic studies of PSO are also discussed.

Molecular basis for enzymatic sulfite oxidation: How three conserved active site residues shape enzyme activity

Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2–3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDHR55M and SDHH57A are relatively insensitive to pH (∼60 and 200 s–1, respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.

Role of Conserved Tyrosine 343 in Intramolecular Electron Transfer in Human Sulfite Oxidase

Tyrosine 343 in human sulfite oxidase (SO) is conserved in all SOs sequenced to date. Intramolecular electron transfer (IET) rates between reduced heme (FeII) and oxidized molybdenum (MoVI) in the recombinant wild-type and Y343F human SO were measured for the first time by flash photolysis. The IET rate in wild-type human SO at pH 7.4 is about 37% of that in chicken SO with a similar decrease in k cat. Steady-state kinetic analysis of the Y343F mutant showed an increase inK m sulfite and a decrease ink cat resulting in a 23-fold attenuation in the specificity constantk cat/K m sulfiteat the optimum pH value of 8.25. This indicates that Tyr-343 is involved in the binding of the substrate and catalysis within the molybdenum active site. Furthermore, the IET rate constant in the mutant at pH 6.0 is only about one-tenth that of the wild-type enzyme, suggesting that the OH group of Tyr-343 is vital for efficient IET in SO. The pH dependences of IET rate constants in the wild-type and mutant SO are consistent with the previously proposed coupled electron-proton transfer mechanism.