Structure and function of mononuclear molybdenum enzymes

 An account of recent advances in our understanding of enzymes possessing mononuclear molybdenum active sites is presented. On the basis of a variety of structural studies, and in conjunction with comparisons among the growing number of these enzymes for which the amino acid sequences are known, it is evident that these enzymes fall into three principal families as represented by xanthine oxidase, sulfite oxidase and DMSO reductase. Structural features of the active sites of these three families are compared and contrasted, and specific mechanistic implications of the recently reported crystal structure for the aldehyde oxidoreductase from Desulfovibrio gigas are discussed. Received: 9 April 1996 / Accepted: 14 June 1996     

Functional models for mononuclear nonheme iron enzymes

Increasing interest in mononuclear nonheme iron enzymes that activate dioxygen has resulted in an explosion of information on such enzymes in recent years. Concomitantly, efforts to model the active sites of these enzymes have produced synthetic complexes capable of mimicking some aspect of the reactivity of the metal center in several enzymes. These functional models carry out oxidative transformations analogous to those catalyzed by the enzymes and in some cases allow iron(III)-peroxo or iron(IV)-oxo intermediates to be trapped and characterized.     

Models for deploymerizing enzymes: criteria for discrimination of models

Several models for the action of alpha amylase have been proposed to account for the nonrandom distribution of oligosaccharides in the amylase digests of polysaccharides. The preferred-attack model attempts to account for the nonrandom distribution by assuming that the probability for bond cleavage depends upon the position of the bond in the chain. The repetitive, or multiple-attack, model suggests that the nonrandom distribution of oligosaccharides arises because an amylase can form a cage-like complex with a substrate and attack it several times during a single encounter. The multiple-enzyme or dual-site model suggests that the nonrandom yield of oligosaccharides arises from the combined action of exo- and endo-enzymes. The effects of pH, inhibitors, and substrate chain-length on enzyme action have been studied in several laboratories to determine which of the three action-patterns best describes the action of alpha amylase. The influence of these variables on product distributions or enzyme action-patterns are mathematically modeled in the Appendix. The experimental data on porcine-pancreatic alpha amylase are discussed in the light of the derivations.     

Incorporation of molybdenum into the iron-molybdenum cofactor of nitrogenase.

The biosynthesis of the iron-molybdenum cofactor (FeMo-co) of dinitrogenase was investigated using 99Mo to follow the incorporation of Mo into precursors. 99Mo label accumulates on dinitrogenase only when all known components of the FeMo-co synthesis system, NifH, NifNE, NifB-cofactor, homocitrate, MgATP, and reductant, are present. Furthermore, 99Mo label accumulates only on the gamma protein, which has been shown to serve as a chaperone/insertase for the maturation of apodinitrogenase when all known components are present. It appears that only completed FeMo-co can accumulate on the gamma protein. Very little FeMo-co synthesis was observed when all known components are used in purified forms, indicating that additional factors are required for optimal FeMo-co synthesis. 99Mo did not accumulate on NifNE under any conditions tested, suggesting that Mo enters the pathway at some other step, although it remains possible that a Mo-containing precursor of FeMo-co that is not sufficiently stable to persist during gel electrophoresis occurs but is not observed. 99Mo accumulates on several unidentified species, which may be the additional components required for FeMo-co synthesis. The molybdenum storage protein was observed and the accumulation of 99Mo on this protein required nucleotide.     

Basic models for differential inhibition of enzymes

The possible preferential action exerted by an inhibitor on the transformation of one of two agonist substrates catalyzed by the same enzyme has recently been reported in studies on aldose reductase inhibition. This event was defined as “intra-site differential inhibition” and the molecules able to exert this action as “differential inhibitors”. This work presents some basic kinetic models describing differential inhibition. Using a simple analytic approach, the results show that differential inhibition can occur through either competitive or mixed type inhibition in which the inhibitor prevalently targets the free enzyme. The results may help in selecting molecules whose differential inhibitory action could be advantageous in controlling the activity of enzymes acting on more than one substrate.     

Investigations of the thermostability of rubredoxin models using molecular dynamics simulations.

The affects of differences in amino acid sequence on the temperature stability of the three-dimensional structure of the small beta-sheet protein, rubredoxin (Rd), was revealed when a set of homology models was subjected to molecular dynamics simulations at relatively high temperatures. Models of Rd from the hyperthermophile, Pyrococcus furiosus (Pf), an organism that grows optimally at 100 degrees C, were compared to three mesophilic Rds of known X-ray crystal structure. Simulations covering the limits of known Rd thermostabilities were carried out at temperatures of 300 K, 343 K, 373 K, and 413 K. They suggest that Rd stability is correlated with structural dynamics. Because the dynamic behavior of three Pf Rd models was consistently different from the dynamic behavior of the three mesophilic Rd structures, detailed analysis of the temperature-dependent dynamic behavior was carried out. The major differences between the models of the protein from the hyperthermophile and the others were: (1) an obvious temperature-dependent transition in the mesophilic structures not seen with the Pf Rd models, (2) consistent AMBER energy for the Pf Rd due to differences in nonbonded interaction terms, (3) less variation in the average conformations for the Pf Rd models with temperature, and (4) the presence of more extensive secondary structure for the Pf Rd models. These unsolvated dynamics simulations support a simple, general hypothesis to explain the hyperthermostability of Pf Rd. Its structure simplifies the conformational space to give a single minimum accessible over an extreme range of temperatures, whereas the mesophilic proteins sample a more complex conformational space with two or more minima over the same temperature range.     

Model studies for molybdenum enzymes. The reduction of cytochrome c by molybdenum(V)-cysteine complexes.

The reduction of ferricytochrome c by two molybdenum(V)-cysteine complexes has been investigated as a model for electron transfer in the molybdenum enzymes sulfite oxidase and nitrate reductase. The reduction by the dioxo-bridged Mo(V)-cysteine complex, di-mu-oxo-bis-[oxo(L-cysteinato)molybdate(V)] (I), is relatively slow and its rate is first order in cyt cIII and zero order in I (k = (1.09 +/- 0.10) times 10(-3) sec minus 1, pH 7.5, 20 degrees). The reduction by the monoxo-bridged complex, mu-oxo-bis[oxodihydroxo(L-cysteinato)molybdate(V)] (II), is extremely rapid and its rate is first order in both reactants (k = (2.6 +/- 0.7) times 10(7) M minus 1 sec minus 1, pH 7.0, 25 degrees). Above pH 7.5, the reduction by II follows biphasic kinetics due to the fast reduction of a low pH form of cyt cIII and a slower reduction of a high pH form (at pH 10.0, 25 degrees, k = 2.9 times 10(6) M minus 1 sec minus 1 for the low pH form and k = 7.2 times 10(4) M minus 1 sec minus 1 for the high pH form). Reaction mechanisms for reductions by both I and II are proposed and the biological implications of the results, both for sulfite oxidase and mechanisms of electron transfer to cytochrome c, are discussed.     

Substrate-activated zinc binding of metallo-beta -lactamases: physiological importance of mononuclear enzymes

We have investigated the influence of substrate binding on the zinc ion affinity of representatives from the three metallo-beta-lactamase subclasses, B1 (BcII from Bacillus cereus and BlaB from Chryseobacterium meningosepticum), B2 (CphA from Aeromonas hydrophila), and B3 (L1 from Stenotrophomonas maltophilia). By competition experiments with metal-free apoenzymes and chromophoric zinc chelators or EDTA, we determined the dissociation constants in the absence and presence of substrates. For the formation of the monozinc enzymes we determined constants of 1.8, 5.1, 0.007, and 2.6 nm in the absence and 13.6, 1.8, 1.2, and 5.7 pm in the presence of substrates for BcII, BlaB, CphA, and L1, respectively. A second zinc ion binds in the absence (presence) of substrates with considerably higher dissociation constants, namely 1.8 (0.8), 0.007 (0.025), 50 (1.9), and 0.006 (0.12) microm for BcII, BlaB, CphA, and L1, respectively. We have concluded that the apo form might be the prevailing state of most of the metallo-beta-lactamases under physiological conditions in the absence of substrates. Substrate availability induces a spontaneous self-activation due to a drastic decrease of the dissociation constants, resulting in the formation of active mononuclear enzymes already at picomolar free zinc ion concentrations. In the presence of substrates, the binuclear state of the enzymes only exists at unphysiologic high zinc concentrations and might be of no biological relevance. From the competition experiments with EDTA it is further concluded that the reactivation rate does not depend on the pool of free zinc ions but proceeds via the EDTA-Zn(II)-enzyme ternary complexes.     

Viscoelastic models for enzymes with multiple conformational states

In this article we represent an enzyme capable of exhibiting more than one conformational state as a viscoelastic unit embedded in a fluid medium. We show how this viscoelastic unit is thermally activated to make transitions between equilibrium states, and propose this model as a mesoscopic representation for transitions between conformational states of an enzyme. In this representation, kinetic constants for transitions between conformations are given explicitly in terms of interactions between the enzyme and the medium. Two applications of this model are discussed: mnemonic enzymes, and co-operative enzymes exhibiting half-of-the-sites reactivity.     

Molecular models for shikimate pathway enzymes of Xylella fastidiosa

The Xylella fastidiosa is a bacterium that is the cause of citrus variegated chlorosis (CVC). The shikimate pathway is of pivotal importance for production of a plethora of aromatic compounds in plants, bacteria, and fungi. Putative structural differences in the enzymes from the shikimate pathway, between the proteins of bacterial origin and those of plants, could be used for the development of a drug for the control of CVC. However, inhibitors for shikimate pathway enzymes should have high specificity for X. fastidiosa enzymes, since they are also present in plants. In order to pave the way for structural and functional efforts towards antimicrobial agent development, here we describe the molecular modeling of seven enzymes of the shikimate pathway of X. fastidiosa. The structural models of shikimate pathway enzymes, complexed with inhibitors, strongly indicate that the previously identified inhibitors may also inhibit the X. fastidiosa enzymes.     

Insights into the nature of Mo(V) species in solution: Modeling catalytic cycles for molybdenum enzymes

The tris(pyrazolyl)borate and related tripodal N-donor ligands originally developed by Trofimenko stabilize mononuclear compounds containing Mo^VIO₂, Mo^VIO, Mo^VO, and Mo^IVO units and effectively inhibit their polynucleation in organic solvents. Dioxo-Mo(VI) complexes of the type LMoO₂(SPh), where L = hydrotris(3,5-dimethylpyrazol-1-yl)borate (Tp^∗), hydrotris(3-isopropylpyrazol-1-yl)borate (Tp^iPr), and hydrotris(3,5-dimethyl-1,2,4-triazol-1-yl)borate (Tz) and related derivatives are the only model systems that mimic the complete reaction sequence of sulfite oxidase, in which oxygen from water is ultimately incorporated into product. The quasi-reversible, one-electron reduction of Tp^∗MoO₂(SPh) in acetonitrile exhibits a positive potential shift upon addition of a hydroxylic proton donor, and the magnitude of the shift correlates with the acidity of the proton donor. These reductions produce two Mo(V) species, [Tp^∗Mo^VO₂(SPh)]⁻ and Tp^∗Mo^VO(OH)(SPh), that are related by protonation. Measurement of the relative amounts of these two Mo(V) species by EPR spectroscopy enabled the pK_a of the Mo^V(OH) unit in acetonitrile to be determined and showed it to be several pK_a units smaller than that for water in acetonitrile. Similar electrochemical-EPR experiments for Tp^iPrMoO₂(SPh) indicated that the pK_a for its Mo^V(OH) unit was ∼1.7 units smaller than that for Tp^∗Mo^VO(OH)(SPh). Density functional theory calculations also predict a smaller pK_a for Tp^iPrMo^VO(OH)(SPh) compared to Tp^∗Mo^VO(OH)(SPh). Analysis of these results indicates that coupled electron-proton transfer (CEPT) is thermodynamically favored over the indirect process of metal reduction followed by protonation. The crystal structure of Tp^iPrMoO₂(SPh) is also presented.     

Sulfur ligation in copper enzymes and models

Biological copper-sulfur entities display versatile and unusual coordination chemistry. The role of the sulfur ligation is briefly reviewed through examples from selected copper enzymes and relevant biomimetic models. Copper thiolate complexes are of particular interest because of their key roles in a number of ubiquitous metalloenzymes such as Type I (blue copper proteins) or in the binuclear Cu(A) electrons transfer site found in both cytochrome c oxidase (CcO) and nitrous oxide reductase (N2OR). The possible roles of the S(Met) ligand in monoxygenases are described in relation to recently proposed pathways. Some prospective regarding the biological relevance of disulfide copper ligation and possible radical copper bonds in catalytic cycle are also discussed.     

Activities of thiamine-dependent enzymes in two experimental models of thiamine-deficiency encephalopathy:

Chronic thiamine deprivation in the rat leads to selective neuropathological damage in brainstem structures whereas treatment with the central thiamine antagonist, pyrithiamine, results in more widespread damage. In order to further elucidate the neurochemical mechanisms responsible for this selective damage, the thiamine-dependent enzyme complex pyruvate dehydrogenase (PDHC) was measured in 10 brain structures in the rat during progression of thiamine deficiency produced by chronic deprivation or by pyrithiamine treatment. Feeding of a thiamine-deficient diet to adult rats resulted in 5–7 weeks in ataxia and loss of righting reflex accompanied by decreased blood transketolase activities. PDHC activities were selectively decreased by 15–30% in midbrain and pons (lateral vestibular nucleus). Thiamine treatment of symptomatic rats led to reversal of neurological signs and to concomitant reductions of the cerebral PDHC abnormalities. Daily pyrithiamine treatment led within 3 weeks to loss of righting reflex and convulsions and to decreased blood transketolase of a comparable magnitude to that observed in chronic thiamine-deprived rats. No significant regional alterations of PDHC, however, were observed in pyrithiamine-treated rats.