Enzyme DMSO reductase

The pH-dependence is of particular relevance for groups that occur in three subsequent oxidation states because the two reduction potentials j° and E° in Equation 13.14 in general have different pH dependence. For example, the paramagnetic Wv state of the tungsto-enzyme DMSO reductase affords an EPR signal with a maximal spin count of 40% of protein concentration at pH = 5 when E° - E° +10 mV, whereas at pH = 8 no signal is detected at all because E° E° (Hagedoorn et al. 2003). 

In this article, we have reviewed computational efforts to study the three typical examples of mono-nuclear Mo enzymes, DMSO reductase, sulfite oxidase and xanthine oxidase. Our focus has been on the computational challenges offered both by enzymatic systems in general and in these Mo enzymes in particular. 

The enzymes that utilize molybdenum can be grouped into two broad categories (1) the nitrogenases, where Mo is part of a multinu-clear metal center, or (2) the mononuclear molybdenum enzymes, such as xanthine oxidase (XO), dimethyl sulfoxide (DMSO) reductase, formate dehydrogenase (FDH), and sulfite oxidase (SO). The last... 

The three known crystal structures of molybdopterin-containing enzymes are from members of the first two families the aldehyde oxido-reductase from D. gigas (MOP) belongs to the xanthine oxidase family (199, 200), whereas the DMSO reductases from Rhodobacter (R.) cap-sulatus (201) and from/ , sphaeroides (202) and the formate dehydrogenase from E. coli (203) are all members of the second family of enzymes. There is a preliminary report of the X-ray structure for enzymes of the sulfite oxidase family (204). 

McEwan AG, IP Ridge, CA McDevitt, P Hugenholtz (2002) The DMSO reductase family of microbial molybdenum enzymes molecular properties and the role in the dissimilatory reduction of toxic elements. 

Fe 2S], a [4Fe-4S] and a [3Fe-4S] center. The enzyme catalyzes the reversible redox conversion of succinate to fumarate. Voltammetry of the enzyme on PGE electrodes in the presence of fumarate shows a catalytic wave for the reduction of fumarate to succinate (much more current than could be accounted for by the stoichiometric reduction of the protein active sites). Typical catalytic waves have a sigmoidal shape at a rotating disk electrode, but in the case of succinate dehydrogenase the catalytic wave shows a definite peak. This window of optimal potential for electrocatalysis seems to be a consequence of having multiple redox sites within the enzyme. Similar results were obtained with DMSO reductase, which contains a Mo-bis(pterin) active site and four [4Fe 4S] centers. 

Figure 17.2 The structure of the pterin cofactor (1) which is common to most molybdenum- and tungsten-containing enzymes and schematic active site structures for members of the xanthine oxidase (2,3), sulfite oxidase (4) and DMSO reductase (5-7) enzyme families. (From Enemark et al., 2004. Copyright (2004) American Chemical Society.)...

In the case of the DMSO reductase family, as pointed out above, the metal centre is bound to two molecules of the cofactor. DMSO reductase itself catalyses the reduction of dimethylsulfoxide to dimethylsulfide with incorporation of the oxygen atom of DMSO into water. The active site of the oxidized enzyme is an L2MoVI0(0-Ser) centre, which, upon reduction, loses the M=0 ligand to give a L2MoIV(0-Ser) centre. In the catalytic... 

The reduction of DMSO catalyzed by molybdenum is an important step in the process of anaerobic respiration carried out by a number of bacteria (169). Much like sulfite oxidase, early MCD studies of DMSO reductase were complicated by the presence of heme iron (173). The discovery of two enzymes that do not include an iron center led to the measurement of MCD spectra of Rhodobacter sphaeroides DMSO reductase that could be assigned exclusively in terms of transitions of the Mo site (Fig. 10b) (174). The six major peaks are assigned as LMCT transitions from the three highest energy occupied orbitals to the two lowest unoccupied orbitals (174). 

The active site structures of the three classes of molybdenum-containing enzymes are compared in Fig. 16-32. In the DMSO reductase family there are two identical molybdopterin dinucleotide coenzymes complexed with one molybdenum. However, only one of these appears to be functionally linked to the Fe2S2 center. 

Dimethyl sulfoxide reductases from both R. sphaeroides and R. capsulatus have been the subject of several x-ray studies [112-115], In addition, extensive resonance Raman (RR) [119,125] and EXAFS studies [126,127] of both oxidized and reduced enzymes have been reported. Despite these studies, there is no single fully accepted picture for the active site of dmso reductase and its transformations during turnover. The following discussion outlines the structural features of the active site and the cofactor that are common to the various analyses as well as the current points of contention. 

The most recent x-ray and EXAFS studies of dmso reductase (R. sphaero-ides) used enzyme crystals grown in the presence of excess dimethylsulfide [126], The reduced molybdenum site is apparently seven-coordinate with a bound dmso (Figure 12). The Mo=0 bond length is 1.7 A (1.6 A x-ray) the Mo—0 bond distances of the dmso and serine are each = 2.0 A. The Mo—S bond distances were 2.4-2.5 A. 

Protein sequence homology suggests that sulfite oxidase and assimilatory nitrate reductase are members of the same molybdenum enzyme subfamily [31]. Consistent with this classification, the cofactors of sulfite oxidase and assimilatory nitrate reductase differ significantly from those in dmso reductase, aldehyde oxido-reductase, xanthine oxidase (see Section IV.E.), and even respiratory nitrate reductase (Section IV.D). The EXAFS of both sulfite oxidase [132-136] and assimilatory nitrate reductase [131,137,138] and x-ray studies of sulfite oxidase (chicken liver) [116] confirm that the molybdenum center is coordinated by two sulfur atoms from a single MPT ligand and by the sulfur atom of a cysteine side chain. The Movl state is bis(oxido) coordinated (Figure 14). 

The bis(l,2-enedithiolate) complexes discussed closely resemble the metal centers found in the dmso reductase family of Mo enzymes and in the tungsten enzymes. The reactivity of mono(l,2-enedithiolate) complexes remains a continuing challenge as synthetic chemists pursue accurate models for the xanthine oxidase and sulfite oxidase families of metal sites. New 1,2-dithiolate ligands [70,71] and complexes are needed to demonstrate ligand effects to help elucidation reaction mechanism. 

Mechanisms of action for the metal centers in acetylene hydratase, polysulfide reductase, and formate dehydrogenase have been briefly described in Sections VI.A and VLB. The discussion, in each case, was relatively straightforward insofar as the natures of these reactions lend themselves to simple mechanistic proposals. The mechanism by which the metal centers function in most of the other Mo and W enzymes is not as obvious. We elect to discuss mechanistic roles for the molybdenum centers in xanthine oxidase, sulfite oxidase, and dmso reductase. These enzymes are representative members of each large class of molybdenum enzymes, and the large body of literature on each enzyme makes detailed discussion possible. 

However, other studies show that reduction of dmso reductase in the absence of excess product yields what appears to be a des(oxido) molybdenum with a metal-bound hydroxido ligand [115], If dmso were to hydrogen bond to this ligand, CEPT transfer linked to water loss could also generate the mono(oxido) oxidized form of the enzyme (Figure 31). 

Figure 2. Aerobic catabolism of methylated sulfides (adapted from Kelly, 1988). 1) DMSO reductase (Hyphomicrobium sp.) 2) DMDS reductase (Thiobacillus sp. 3) trimethylsulfonium-tetrahydrofolate methyltransferase (Pseudomonas sp.) 4) DMS monooxygenase 5) methanethiol oxidase 6) sulfide oxidizing enzymes 7) catalase 8) formaldehyde dehydrogenase 9) formate dehydrogenase 10) Calvin cycle for CO2 assimilation (Thiobacillus sp.) 11) serine pathway for carbon assimilation (Hyphomicrobium sp.).

Figure 16. Consensus oxidized active-site structures of the xanthine oxidase (XO), sulfite oxidase (SO), and DMSO reductase (DMSOR), and aldehyde oxidoreductase (AOR) families of mononuclear molybdenum and tungsten enzymes and the structure of the common ppd cofactor (41, 42). The question mark in the AOR structure indicates uncertainty in the presence of a coordinated water molecule.

Figure 2. The ligand common to all molybdenum and tungsten enzymes, MPT, is shown here in several formats (a) in common stick notation (b) as a ball and stick (c) an orientation rotated 90° from view (b) to emphasize the spacial relationship between the pterin plane and the dithiolene-pyran ring portion (d) MGD in common stick notation and for comparison, (e ) FAD, a common electron-transfer prosthetic group. Coordinates for the views in (b) and (c) are taken from the data deposited in the Protein Data Bank (PDB) for the 1.3-A resolution structure of DMSO reductase from Rhodobacter sphaeroides.

Valuable spectroscopic studies on the dithiolene chelated to Mo in various enzymes have been enhanced by the knowledge of the structure from X-ray diffraction. Plagued by interference of prosthetic groups—heme, flavin, iron-sulfur clusters—the majority of information has been gleaned from the DMSO reductase system. The spectroscopic tools of X-ray absorption spectroscopy (XAS), electronic ultraviolet/visible (UV/vis) spectroscopy, resonance Raman (RR), MCD, and various electron paramagnetic resonance techniques [EPR, electron spin echo envelope modulation (ESEEM), and electron nuclear double resonance (ENDOR)] have been particularly effective probes of the metal site. Of these, only MCD and RR have detected features attributable to the dithiolene unit. Selected results from a variety of studies are presented below, chosen because their focus is the Mo-dithiolene unit and organized according to method rather than to enzyme or type of active site. 

A few representative Mo enzymes are listed in Table 18-C-6. Note that most have very high molecular weights, and this has delayed structure determinations. In the case of DMSO-reductase, however, the lower molecular weight has made possible a structure determination. The Mo site is found to be as shown in 18-C-XXVII. In a tungsten-containing enzyme, ferredoxin aldehyde oxidoreductase, the metal site is as shown in 18-C-XXVIII. 

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