Effect of the protein ligand in DMSO reductase studied by computational methods
The DMSO reductase family is the largest and most diverse family of mononuclear molybdenum oxygen-atom-transfer proteins. Their active sites contain a Mo ion coordinated to two molybdopterin ligands, one oxo group in the oxidised state, and one additional, often protein-derived ligand. We have used density-functional theory to evaluate how the fourth ligand (serine, cysteine, selenocysteine, OH-, O2-, SH-, or S2-) affects the geometries, reaction mechanism, reaction energies, and reduction potentials of intermediates in the DMSO reductase reaction. Our results show that there are only small changes in the geometries of the reactant and product states, except from the elongation of the MoX bond as the ionic radius of XO, S, Se increases. The five ligands with a single negative charge gave an identical two-step reaction mechanism, in which DMSO first binds to the reduced active site, after which the SO bond is cleaved, concomitantly with the transfer of two electrons from Mo in a rate-determining second transition state. The five models gave similar activation energies of 69-85kJ/mol, with SH- giving the lowest barrier. In contrast, the O2- and S2- ligands gave much higher activation energies (212 and 168kJ/mol) and differing mechanisms (a more symmetric intermediate for O2- and a one-step reaction without any intermediate for S2-). The high activation energies are caused by a less exothermic reaction energy, 13-25kJ/mol, and by a more stable reactant state owing to the strong MoO2- or MoS2- bonds.
Dong, G., and Ryde, U.,Effect of the protein ligand in DMSO reductase studied by computational methods, Journal of inorganic biochemistry, 2017, 171, 45-51.
Dimethyl sulfoxide (DMSO) reductase
The molybdenum site of the oxidized Mo(VI) dimethyl sulfoxide (DMSO) reductase enzyme possesses one terminal oxygen ligand (Mo=O) at 1.68 Angstrom, four thiolate ligands at 2.44 Angstrom, and one oxygen at 1.92 Angstrom. The dithionite-reduced Mo(IV) enzyme possesses a desoxo species with three or four Mo-S at 2.33 Angstrom and two different Mo-O ligands at 2.16 and 1.92 Angstrom. One exchangeable oxygen ligand, most likely an Mo- OH, in the ESR-active signal-giving species originates from the Mo=O of the oxidized enzyme. The enzyme reduced by dimethylsulfide contains a desoxo active site with four Mo-S at 2.36 and two different Mo-O ligands at 1.94 and 2.14 Angstrom. Recombinant wild-type R. sphaeroides DMSO reductase expressed in Escherichia coli. initially has a dioxo structure (two Mo=O at 1.72 Angstrom and four Mo-S at 2.48 Angstrom) but assumes the wild-type Mo(VI) structure after a cycle of reduction and reoxidation. The site-directed Ser147-->Cys mutant possesses a monooxo active site in the oxidized state (Mo=O at 1.70 Angstrom) with five sulfur ligands (at 2.40 Angstrom), consistent with cysteine 147 coordination to Mo. The dithionite reduced form of the mutant possesses a desoxo site also with five. Mo-S ligands (at 2.37 Angstrom) and one Mo-O at 2.12 Angstrom.
George, G.N., Hilton, J., Temple, C., Prince, R.C., Rajagopalan, K.V., Structure of the molybdenum site of dimethyl sulfoxide reductase, Journal Of The American Chemical Society, 1999, 121, 1256-1266.
Dimethyl sulfoxide (DMSO) reductase from purple bacteria contains a mononuclear Mo co-ordinated by two molybdopterin guanine dinucleotides as its single cofactor. Crystallographic studies on the enzyme from Rhodobacter sphaeroides and Rhodobacter capsulatus revealed substantial differences in the Mo co-ordination environment in the oxidized Mo(VI) state, despite a close structural similarity in the overall fold of the protein. The crystal structure of DMSO reductase from R. sphaeroides identified a Mo environment with a mono-oxo ligation and an asymmetric co-ordination by the two molybdopterins, with three short and one very long Mo-S bond.
In contrast, two independent crystallographic studies of the enzyme from R. capsulatus revealed two additional Mo co-ordination environments: a pentacoordinated dioxo metal ligation sphere in which one molybdopterin is completely dissociated from the Mo and a heptacoordinated environment with symmetrical metal co-ordination by both molybdopterins and two oxo ligands. In all three structures the side chain of a serine was a ligand to the Mo. EXAFS studies on the R. sphaeroides enzyme suggested a hexacoordinated active site geometry, whereas for the R. capsulatus enzyme EXAFS indicated seven ligands.
Baugh, P.E., Garner, C.D., Charnock, J.M., Collison, D., Davies, E.S., McAlpine, A.S., Bailey, S., Lane, I., Hanson, G.R., McEwan, A.G, X-ray absorption spectroscopy of dimethylsulfoxide reductase from Rhodobacter capsulatus, Journal Of Biological Inorganic Chemistry, 1997, 2, 634-643.
The 1.3 Angstrom resolution crystal structure of oxidized DMSOR from R. sphaeroides reveals plasticity at the active site. The Mo is discretely disordered and exists in a hexacoordinated and a pentacoordinated ligation sphere. The hexacoordinated model reconciles the existing differences in active site co-ordination of R. sphaeroides DMSO reductase as studied by crystallographic and EXAFS techniques. In addition, the pentacoordinated structure closely resembles one of the reported R. capsulatus crystal structures.
Trieber, C.A., Rothery, R.A., Weiner, J.H., Consequences Of Removal Of A Molybdenum Ligand (Dmsa-Ser-176) Of Escherichia-Coli Dimethyl-Sulfoxide Reductase, Journal Of Biological Chemistry, 1996, 271, 27339-27345.
The active site geometry in the previously reported 2.2 Angstrom crystal structure of R, sphaeroides DMSO reductase appears to represent an average of the two conformations described here. Thus, structural flexibility at the active site appears to give rise to the observed differences in the Mo co-ordination environment
Li, H.K., Temple , C., Rajagopalan, K. V., and Schindelin, H., The 1.3 angstrom crystal structure of Rhodobacter sphaeroides dimethyl sulfoxide reductase reveals two distinct molybdenum co-ordination environments, Journal of the American Chemical Society, 2000, 122, 7673-7680.
Dimethylsulfoxide reductase ― molybdenum coordination in the reduced enzyme
Reduced dimethylsulfoxide reductase (DMSOR) enzymes have an active-site which (a) lacks a terminal oxo ligand (unlike the reduced active sites of other pyranopterin Mo enzymes); (b) has two pyranopterin-ene-1,2-dithiolate ligands (unlike other pyranopterin Mo enzymes but analogous to all of the currently known tungsten-containing enzymes). The Mo-bisdithiolene electronic structure and bonding in the absence of a strong-field oxo ligand is discussed in relation to the electronic and Raman spectra of model complexes.
McNaughton, R.L., Lim, B. S., Knottenbelt, S. Z., Holm, R. H., and Kirk, M. L., Spectroscopic and electronic structure studies of symmetrized models for reduced members of the dimethylsulfoxide reductase enzyme family, Journal of the American Chemical Society, 2008, 130, 4628-4636.