Domain swapping in allosteric modulation of DNA specificity.

SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-modulation of cleavage activity and sequence specificity. Previous studies have shown that DNA bound dimers of SgrAI oligomerize into an activated form with higher DNA cleavage rates, although previously determined crystal structures of SgrAI bound to DNA show only the DNA bound dimer. A new crystal structure of the type II restriction endonuclease SgrAI bound to DNA and Ca(2+) is now presented, which shows the close association of two DNA bound SgrAI dimers. This tetrameric form is unlike those of the homologous enzymes Cfr10I and NgoMIV and is formed by the swapping of the amino-terminal 24 amino acid residues. Two mutations predicted to destabilize the swapped form of SgrAI, P27W and P27G, have been made and shown to eliminate both the oligomerization of the DNA bound SgrAI dimers as well as the allosteric stimulation of DNA cleavage by SgrAI. A mechanism involving domain swapping is proposed to explain the unusual allosteric properties of SgrAI via association of the domain swapped tetramer of SgrAI bound to DNA into higher order oligomers.

Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.

The functional and structural consequences of a mutation of the DNA intercalating residue of HincII, Q138F, are presented. Modeling has suggested that the DNA intercalation by Gln-138 results in DNA distortions potentially used by HincII in indirect readout of its cognate DNA, GTYRAC (Y = C or T, R = A or G) (Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47). Kinetic data presented here indicate that the mutation of glutamine 138 to phenylalanine (Q138F) results in a change in sequence specificity at the center two base pairs of the cognate recognition site. We show that the preference of HincII for cutting, but not binding, the three cognate sites differing in the center two base pairs has been altered by the mutation Q138F. Five new crystal structures are presented including Q138F HincII bound to GTTAAC and GTCGAC both with and without Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The Q138F HincII/DNA structures show conformational changes in the protein, bound DNA, and at the protein-DNA interface, consistent with the formation of adaptive complexes. Analysis of these structures and the effect of Ca2+ binding on the protein-DNA interface illuminates the origin of the altered specificity by the mutation Q138F in the HincII enzyme.

Understanding the origin of metal-sulfur vibrations in an oxo-molybdenum dithiolene complex: relevance to sulfite oxidase.

X-ray crystallography and resonance Raman (rR) spectroscopy have been used to further characterize (Tp*)MoO(qdt) (Tp* is hydrotris(3,5-dimethyl-1-pyrazolyl)borate and qdt is 2,3-quinoxalinedithiolene), which represents an important benchmark oxomolybdenum mono-dithiolene model system relevant to various pyranopterin Mo enzyme active sites, including sulfite oxidase. The compound (Tp*)MoO(qdt) crystallizes in the triclinic space group, P1, where a = 9.8424 (7) A, b = 11.2323 (8) A, c = 11.9408 (8) A, alpha = 92.7560 (10) degrees, beta = 98.9530 (10) degrees, and gamma = 104.1680 (10) degrees. The (Tp*)MoO(qdt) molecule exhibits the distorted six-coordinate geometry characteristic of related oxo-Mo(V) systems possessing a single coordinated dithiolene ligand. The first coordination sphere bond lengths and angles in (Tp*)MoO(qdt) are very similar to the corresponding structural parameters for (Tp*)MoO(bdt) (bdt is 1,2-benzenedithiolene). The relatively small inner-sphere structural variations observed between (Tp*)MoO(qdt) and (Tp*)MoO(bdt) strongly suggest that geometric effects are not a major contributor to the significant electronic structural differences reported for these two oxo-Mo(V) dithiolenes. Therefore, the large differences observed in the reduction potential and first ionization energy between the two molecules appear to derive primarily from differences in the effective nuclear charges of their respective sulfur donors. However, a subtle perturbation to Mo-S bonding is implied by the nonplanarity of the dithiolene chelate ring, which is defined by the fold angle. This angular distortion (theta = 29.5 degrees in (Tp*)MoO(qdt); 21.3 degrees in (Tp*)MoO(bdt)) observed between the MoS2 and S-C=C-S planes may contribute to the electronic structure of these oxo-Mo dithiolene systems by controlling the extent of S p-Mo d orbital overlap. In enzymes, the fold angle may be dynamically modulated by the pyranopterin, thereby functioning as a transducer of vibrational energy associated with protein conformational changes directly to the active site via changes in the fold angle. This process could effectively mediate charge redistribution at the active site during the course of atom- and electron-transfer processes. The rR spectrum shows bands at 348 and 407 cm(-1). From frequency analysis of the normal modes of the model, [(NH3)3MoO(qdt)]1+, using the Gaussian03 suite of programs, these bands are assigned as mixed-mode Mo-S vibrations of the five-membered Mo-ditholene core structure. Raman spectroscopy has also provided additional evidence for an in-plane pseudo-sigma dithiolene S-Mo d(xy) covalent bonding interaction in (Tp*)MoO(qdt) and related oxo-Mo-dithiolenes that has implications for electron-transfer regeneration of the active site in sulfite oxidase involving the pyranopterin dithiolene.

Electronic structure of bent titanocene complexes with chelated dithiolate ligands.

Gas-phase photoelectron spectroscopy and density functional theory have been utilized to investigate the interactions between the p orbitals of dithiolate ligands and d orbitals of titanium in bent titanocene complexes as minimum molecular models of active site features of pyranopterin Mo/W enzymes. The compounds Cp(2)Ti(S-S) [where (S-S) is 1,2-ethenedithiolate (S(2)C(2)H(2)), 1, 1,2-benzenedithiolate (bdt), 2, or 1,3-propanedithiolate (pdt), 3, and Cp(-) is cyclopentadienyl] provide access to a formal 16-electron d(0) electronic configuration at the metal. A "dithiolate-folding-effect" involving an interaction of metal and sulfur orbitals is demonstrated in complexes with arene- and enedithiolates. This effect is not observed for the alkanedithiolate in complex 3.

Geometrical control of the active site electronic structure of pyranopterin enzymes by metal-dithiolate folding: aldehyde oxidase.

Density functional calculations on geometry-optimized oxidized (Mo(VI)) and reduced (Mo(IV)) analogues of the isolated active site of aldehyde oxidase (MOP), a member of the xanthine oxidase family of pyranopterindithiolate enzymes, show that fold angle changes of the dithiolate ligand modulate the relative metal and dithiolate contributions to the frontier redox orbitals. Proton abstraction from the equatorial aqua ligand of the oxidized Mo(VI) site also flattens the metal dithiolate fold angle. It is proposed that static and/or dynamic changes in the structure of the protein surrounding the active site can induce changes in the dithiolate fold angle and thereby provide a mechanism for electronic buffering of the redox orbital, for fine-tuning the nucleophilicity of the equatorial aqua/hydroxide ligand, and for modulating the electron-transfer regeneration of the active sites of molybdenum and tungsten enzymes via a "dithiolate folding effect".

Structural and functional analogue of the active site of polysulfide reductase from Wolinella succinogenes.

Synthesis of [PPh4]2[Mo(SPh)2(S2C2(CN)2)2] (2) from [PPh4]2[MoO(S2C2(CN)2)2] (1) has been achieved to mimic the postulated [Mo(S)6] core of polysulfide reductase with two thiolates and two bis(ene-dithiolate) ligands. Compound 2 reacts with polysulfide to yield H2S, modeling the function of polysulfide reductase. The facile conversion of 2 back to 1 in moist solvent suggests that the interconversion of the [MoIV = O] and [MoIV - X] (X = O-Ser, S-Cys, Se-Cys) moieties might occur in the DMSO reductase class of enzymes under appropriate hydrophobic/hydrophilic conditions.

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 pi-orbitals of arene dithiolates and high-valent transition metals as minimum molecular models of the active site features of pyranopterin MoW enzymes. The compounds (Tp*)MoO(bdt) (compound 1), Cp(2)Mo(bdt) (compound 2), and Cp(2)Ti(bdt) (compound 3) [where Tp* is hydrotris(3,5-dimethyl-1-pyrazolyl)borate, bdt is 1,2-benzenedithiolate, and Cp is eta(5)- cyclopentadienyl] provide access to three different electronic configurations of the metal, formally d(1), d(2), and d(0), 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-pi orbitals is proposed to be a factor in the electron transfer reactions that regenerate the active sites of molybdenum and tungsten enzymes.