Crystal structure of Methanococcus jannaschii dihydroorotase.

In this paper, we report the structural analysis of dihydroorotase (DHOase) from the hyperthermophilic and barophilic archaeon Methanococcus jannaschii. DHOase catalyzes the reversible cyclization of N-carbamoyl-l-aspartate to l-dihydroorotate in the third step of de novo pyrimidine biosynthesis. DHOases form a very diverse family of enzymes and have been classified into types and subtypes with structural similarities and differences among them. This is the first archaeal DHOase studied by x-ray diffraction. Its structure and comparison with known representatives of the other subtypes help define the structural features of the archaeal subtype. The M. jannaschii DHOase is found here to have traits from all subtypes. Contrary to expectations, it has a carboxylated lysine bridging the two Zn ions in the active site, and a long catalytic loop. It is a monomeric protein with a large ß sandwich domain adjacent to the TIM barrel. Loop 5 is similar to bacterial type III and the C-terminal extension is long.

Effect of the Lattice Field on the Electronic Structure and Dynamics of Copper-Hexahydrate in Tutton Salts.

Previous structural and electron paramagnetic resonance (EPR) results are combined with new theoretical chemistry calculations on a series of copper-containing Tutton salts to investigate the influence of the host crystal electric field on the copper unpaired wave function and dynamics. Density functional theory (DFT) computations were performed on clusters centered on the host structure metal-hexahydrate complex to provide a model of atomic charges, which in turn were used to determine the electric fields and potentials at points along coordinate bonds of the complex. A significantly higher electric potential at the metal-water bonds is found for those Tutton salt systems having a greater copper EPR temperature dependency. Such a dependency has long been interpreted to arise from the averaging of tensor coupling parameters of the copper-hexahydrate complex due to a dynamic Jahn-Teller effect. However, the correlation found here reinforces a recent view that the coupling of the copper complex to the surrounding crystal lattice is the major determinant of these dynamics. The lattice potentials lack any significant temperature dependency and thus do not appear to be responsible for changes in the EPR patterns. A trend also appears between unbalanced spin in the compressed d-orbital lobe of the unpaired wave function and the magnitude of the potential. Hence, the lattice field is an important factor in defining both the electronic and dynamic characteristics of the copper-hexahydrate complex in these systems.

Electron Paramagnetic Resonance Characteristics and Crystal Structure of a Tutton Salt Analogue: Copper-Doped Cadmium Creatininium Sulfate.

Electron paramagnetic resonance and crystallographic studies on copper-doped cadmium creatininium sulfate (CdCrnS) were undertaken to study the characteristics of a copper-hexahydrate complex in an organic analogue of Tutton's salt. X-ray diffraction experiments determined the crystal structure of CdCrnS at both 100 and 298 K. CdCrnS, like Tutton salt, crystallizes in the monoclinic space group P21/n. The unit cell contains two cadmium hexahydrate complexes, four creatininium ions, four sulfates, and four additional solvation waters. Both crystallography and EPR find that the doped copper replaces the cadmium in the structure. Single-crystal EPR measurements at room temperature determined the g and copper hyperfine (ACu) tensors (principal values: g = 2.437, 2.134, and 2.080 and ACu = -327, -84.8, and 7.33 MHz). EPR spectra of the powder at room temperature gave g = 2.448, 2.125, and 2.085 and ACu = -315, -75.0, and 35.0 MHz and at 110 K gave g = 2.462, 2.116, and 2.077 and ACu = -340, -30.0, and 35.0 MHz. The room-temperature tensors are close to the "rigid lattice limit" values found in copper-doped Tutton salts but with a higher gmin and weaker ACux coupling than average. A small but measurable temperature dependency of the tensors indicated the presence of a dynamic Jahn-Teller (JT) effect. In addition, the EPR line width changed dramatically with temperature, which is like that found in all copper-doped Tutton crystals. Utilizing the model of Silver-Getz for the g-value variation gave an estimate for the energy difference (δ12 = 640 cm-1) between the ground and next highest JT configurations. An empirical correlation appears to exist between δ12 and gmin and ACux for the copper hexahydrates studied in similar crystals. This suggests a relationship between the amount of unpaired spins in the copper d-orbital x lobe and the gap between wells of the adiabatic potential surface.

Probing Axial Water Bound to Copper in Tutton Salt Using Single Crystal 17O-ESEEM Spectroscopy.

Electron spin-echo envelope modulation (ESEEM) signals attributed to axial water bound to Cu2+ have been detected and analyzed in Cu(II)-doped 17O-water-enriched potassium zinc sulfate hexahydrate (Tutton salt) crystals. The magnetic field orientation dependences of low frequency modulations were measured to fit hyperfine and quadrupole coupling tensors of a 17O ( I = 5/2) nucleus. The hyperfine tensor ( A xx, A yy, A zz: 0.13, 0.23, -3.81 MHz) exhibits almost axial symmetry with the largest value directed normal to the metal equatorial plane in the host structure. Comparisons with quantum chemical calculations position this nucleus about 2.3 Å from the copper. The isotropic coupling (-1.15 MHz) is small and reflects the weak axial water interaction with a dx2-y2 unshared orbital of copper. The 17O-water quadrupole interaction parameters ( e2 qQ/ h = 6.4 MHz and η = 0.93) are close to the average of those found in a variety of solid hydrates. In addition, the coupling tensor directions correlate very closely with the O8 water geometry, with the maximum quadrupole direction 3° from the water plane normal, and its minimum coupling about 2° from the H-H direction. In almost all previous magnetic resonance 17O-water studies, the quadrupole tensor orientation was based on theoretical considerations. This work represents one of the few experimental confirmations of its principal axis frame. When Cu2+ dopes into the Tutton salt, a Jahn-Teller distortion interchanges the relative long and intermediate metal O7 and O8 bond lengths of the zinc host. Therefore, only those unit cells containing the impurity conform to the pure copper Tutton structure. This study provides further support for this model. Moreover, coupling interactions from distant H217O such as in the present case have important implications in studies of copper enzymes and proteins where substrates have been proposed to displace weakly bound water in the active site.

Characterization of the Dihydroorotase from Methanococcus jannaschii.

The gene that codes for the putative dihydroorotase in the hyperthermophilic archaeon Methanococcus jannaschii was subcloned in pET-21a and expressed in Escherichia coli. A purification protocol was devised. The purity of the protein was evaluated by SDS-PAGE and the protein was confirmed by sequencing using LC-MS. The calculated molecular mass is 48104 Da. SEC-LS suggested that the protein is a monomer in solution. ICP-MS showed that there are two Zn ions per monomer. Kinetic analysis of the recombinant protein gave hyperbolic kinetics with Vmax = 12.2 µmol/min/mg and Km = 0.14 mM at 25 °C. Furthermore the activity of the protein increased with temperature consistent with the hyperthermophilic nature of the organism. A homology model was constructed using the mesophilic Bacillus anthracis protein as the template. Residues known to be critical for Zn and substrate binding were conserved. The activity of the enzyme at 85 and 90 °C was found to be relatively constant over 160 min and this correlates with the temperature of optimal growth of the organism of 85 °C. The amino acid sequences and structures of the two proteins were compared and this gave insight into some of the factors that may confer thermostability-more Lys and Ile, fewer Ala, Thr, Gln and Gly residues, and shorter N- and C-termini. Additional and better insight into the thermostabilization strategies adopted by this enzyme will be provided when its crystal structure is determined.

Models for Copper Dynamic Behavior in Doped Cadmium dl-Histidine Crystals: Electron Paramagnetic Resonance and Crystallographic Analysis.

Electron paramagnetic resonance and crystallographic studies of copper-doped cadmium dl-histidine, abbreviated as CdDLHis, were undertaken to gain further understanding on the relationship between site structure and dynamic behavior in biological model complexes. X-ray diffraction measurements determined the crystal structure of CdDLHis at 100 and 298 K. CdDLHis crystallizes in the monoclinic space group P21/c with two cadmium complexes per asymmetric unit. In each complex, the Cd is hexacoordinated to two histidine molecules. Both histidines are l in one complex and d in the other. Additionally, each complex contains multiple waters of varying disorder. Single crystal EPR spectroscopic splitting (g) and copper hyperfine (A(Cu)) tensors at room temperature (principal values: g = 2.249, 2.089, 2.050; A(Cu) = -453, -30.5, -0.08 MHz) were determined from rotational experiments. Alignments of the tensor directions with the host structure were used to position the copper unpaired dx(2)-y(2) orbital in an approximate plane made by four proposed ligand atoms: the N-imidazole and N-amino of one histidine, and the N-amino and O-carboxyl of the other. Each complex has two such planes related by noncrystallographic symmetry, which make an angle of 65° and have a 1.56 Å distance between their midpoints. These findings are consistent with three interpretations that can adequately explain previous temperature-dependent EPR powder spectra of this system: (1) a local structural distortion (static strain) at the copper site has a temperature dependence significant enough to affect the EPR pattern, (2) the copper can hop between the two sites in each complex at high temperature, and (3) there exists a dynamic Jahn-Teller effect involving the copper ligands.

Copper dynamics in doped metal-bis(histidine) complexes.

Electron paramagnetic resonance (EPR) temperature-dependent measurements were undertaken on three Cu(II)-doped metal-histidine complexes to assess copper site dynamic behavior. Previous single-crystal EPR analysis on two of these, zinc d,l-histidine pentahydrate (ZnDLH) and bis(l-histidinato)cadmium dihydrate (CdLH), found that doped Cu(2+) can be modeled as hopping between two neighboring conformational states, with a temperature-dependent rate becoming large enough at room temperature to produce an "averaged" spectrum. By comparing spectra from their powdered form, we show that Cu(2+) doped into a third system, Cd(2+)-d,l-histidine (CdDLH), also exhibits temperature-dependent EPR with features indicating a similar motional-averaging process. In addition, the change of g and copper hyperfine parameters from low to high temperature for CdDLH resembles that in ZnDLH, whereas the change in these parameters for CdLH is like that found in a fourth copper-doped system, zinc l-histidine dihydrate (ZnLH). Taken together, these results suggest that averaging motion between neighboring copper sites is common in metal-bis(histidine) compounds. More detailed studies on biological models are thus warranted, especially because they reveal unique relationships between structure, dynamic processes, and stability and can lead to a better understanding of the role played by site flexibility in copper proteins.

Electron paramagnetic resonance spectroscopic study of copper hopping in doped bis(L-histidinato)cadmium dihydrate.

Electron paramagnetic resonance (EPR) spectroscopy was used to study Cu(II) dynamic behavior in a doped biological model crystal, bis(L-histidinato)cadmium dihydrate, in order to gain better insight into copper site stability in metalloproteins. Temperature-dependent changes in the low temperature X-band EPR spectra became visible around 100 K and continued up to room temperature. The measured 298 K g-tensor (principal values: 2.17, 2.16, 2.07) and copper hyperfine coupling tensor (principal values: -260, -190, -37 MHz) were similar to the average of the 77 K tensor values pertaining to two neighboring histidine binding sites. The observed temperature dependence was interpreted using Anderson's theory of motional narrowing, where the magnetic parameters for the different states are averaged as the copper rapidly hops between sites. The EPR pattern was also found to undergo a sharp sigmoidal-shaped, temperature-dependent conversion between two species with a critical temperature T(c) ≈ 160 K. The species below T(c) hops between the two low temperature site patterns, and the one above T(c) represents an average of the molecular spin Hamiltonian coupling tensors of the two 77 K sites. In addition, the low and high temperature species hop between one another, contributing to the dynamic averaging. Spectral simulations using this 4-state model determined a hop rate between the two low temperature sites ν(h4) = 4.5 × 10(8) s(-1) and between the low and high temperature states ν(h2) = 1.7 × 10(8) s(-1) at 160 K. An Arrhenius relationship of hop rate and temperature gave energy barriers of ΔE4 = 389 cm(-1) and ΔE2 = 656 cm(-1) between the two low temperature sites and between the low and high temperature states, respectively.

Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: insights into the path of carbamoyl phosphate to the active site of the enzyme.

Crystals of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase (ATCase) grew in the presence of the regulatory chain in the hexagonal space group P6(3)22, with one monomer per asymmetric unit. This is the first time that crystals with only one monomer in the asymmetric unit have been obtained; all known structures of the catalytic subunit contain several crystallographically independent monomers. The symmetry-related chains form the staggered dimer of trimers observed in the other known structures of the catalytic subunit. The central channel of the catalytic subunit contains a sulfate ion and a K(+) ion as well as a glycerol molecule at its entrance. It is possible that it is involved in channeling carbamoyl phosphate (CP) to the active site of the enzyme. A second sulfate ion near Arg164 is near the second CP position in the wild-type Escherichia coli ATCase structure complexed with CP. It is suggested that this position may also be in the path that CP takes when binding to the active site in a partial diffusion process at 310 K. Additional biochemical studies of carbamoylation and the molecular organization of this enzyme in M. jannaschii will provide further insight into these points.

Aspects of structure and bonding in copper-amino acid complexes revealed by single-crystal EPR/ENDOR spectroscopy and density functional calculations.

This work deduces from a series of well-defined copper-doped amino acid crystals, relationships between structural features of the copper complexes, and ligand-bound proton hyperfine parameters. These were established by combining results from electron paramagnetic resonance (EPR)/electron-nuclear double resonance (ENDOR) studies, crystallography, and were further assessed by quantum mechanical (QM) calculations. A detailed evaluation of previous studies on Cu(2+) doped into alpha-glycine, triglycine sulfate, alpha-glycylglycine, and L-alanine crystals reveal correlations between geometric features of the copper sites and proton hyperfine couplings from amino-bound and carbon-bound hydrogens. Experimental variations in proton isotropic hyperfine coupling values (a(iso)) could be fit to cosine-square dependences on dihedral angles, namely, for C(alpha)-bound hydrogens, a(iso) = -1.09 + 8.21 cos(2) theta MHz, and for amino hydrogens, a(iso) = -6.16 + 4.15 cos(2) phi MHz. For the C(alpha) hydrogens, this dependency suggests a hyperconjugative-like mechanism for transfer of spin density into the hydrogen 1s orbital. In the course of this work, it was also necessary to reanalyze the ENDOR measurements from Cu(2+)-doped alpha-glycine because the initial study determined the (14)N coupling parameters without holding its nuclear quadrupole tensor traceless. This new treatment of the data was needed to correctly align the (14)N hyperfine tensor principal directions in the molecular complex. To provide a theoretical basis for the coupling variations, QM calculations performed at the DFT level were used to compute the proton hyperfine tensors in the four crystal complexes as well as in a geometry-optimized Cu(2+)(glycine)(2) model. These theoretical calculations confirmed systematic changes in couplings with dihedral angles but greatly overestimated the experimental geometric sensitivity to the amino hydrogen isotropic coupling.

Structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form.

Crystals of the catalytic subunit of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form contain four crystallographically independent trimers which associate in pairs to form stable staggered complexes that are similar to each other and to a previously determined monoclinic C2 form. Each subunit has a sulfate in the central channel. The catalytic subunits in these complexes show flexibility, with the elbow angles of the monomers differing by up to 7.4 degrees between crystal forms. Moreover, there is also flexibility in the relative orientation of the trimers around their threefold axis in the complexes, with a difference of 4 degrees between crystal forms.

Crystal structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase.

The catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase is extremely heat stable, maintaining 75% of its activity after heat treatment for 60 min at 75 degrees C. We undertook its structural analysis in order to understand the molecular basis of its thermostability and gain insight on how its catalytic function adapts to high temperature. Several structural elements potentially contributing to thermostability were identified. These include: (i) changes in the amino acid composition such as a decrease in the thermolabile residues Gln and Asn, an increase in the charged residues Lys and Glu, an increase in Tyr and a decrease in Ala residues; (ii) a larger number of salt bridges, in particular, the improvement of ion-pair networks; (iii) shortening of the N-terminus and shortening of three loops. An interesting feature of the crystal structure is the association of two crystallographically independent catalytic subunits into a staggered complex with an intertrimer distance of 33.8 A. The active site appears similar to Escherichia coli. Upon substrate binding, smaller changes in the global orientation of domains and larger conformational changes of the active site residues are expected as compared to E. coli.

Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1.

The RNA-recognition motif (RRM) is a common and evolutionarily conserved RNA-binding module. Crystallographic and solution structural studies have shown that RRMs adopt a compact alpha/beta structure, in which four antiparallel beta-strands form the major RNA-binding surface. Conserved aromatic residues in the RRM are located on the surface of the beta-sheet and are important for RNA binding. To further our understanding of the structural basis of RRM-nucleic acid interaction, we carried out a high resolution analysis of UP1, the N-terminal, two-RRM domain of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), whose structure was previously solved at 1.75-1.9 A resolution. The two RRMs of hnRNP A1 are closely related but have distinct functions in regulating alternative pre-mRNA splice site selection. Our present 1.1 A resolution crystal structure reveals that two conserved solvent-exposed phenylalanines in the first RRM have alternative side chain conformations. These conformations are spatially correlated, as the individual amino acids cannot adopt each of the observed conformations independently. These phenylalanines are critical for nucleic acid binding and the observed alternative side chain conformations may serve as a mechanism for regulating nucleic acid binding by RRM-containing proteins.