Dithionite treatment of flavins: spectral evidence for covalent adduct formation and effect on in vitro bacterial bioluminescence

The Nonphysiological Reductant Sodium Dithionite and [FeFe] Hydrogenase: Influence on the Enzyme Mechanism

[FeFe] hydrogenases are highly active enzymes for interconverting protons and electrons with hydrogen (H₂). Their active site H-cluster is formed of a canonical [4Fe-4S] cluster ([4Fe-4S]_H) covalently attached to a unique [2Fe] subcluster ([2Fe]_H), where both sites are redox active. Heterolytic splitting and formation of H₂ takes place at [2Fe]_H, while [4Fe-4S]_H stores electrons. The detailed catalytic mechanism of these enzymes is under intense investigation, with two dominant models existing in the literature. In one model, an alternative form of the active oxidized state H_ox, named H_oxH, which forms at low pH in the presence of the nonphysiological reductant sodium dithionite (NaDT), is believed to play a crucial role. H_oxH was previously suggested to have a protonated [4Fe-4S]_H. Here, we show that H_oxH forms by simple addition of sodium sulfite (Na₂SO₃, the dominant oxidation product of NaDT) at low pH. The low pH requirement indicates that sulfur dioxide (SO₂) is the species involved. Spectroscopy supports binding at or near [4Fe-4S]_H, causing its redox potential to increase by ∼60 mV. This potential shift detunes the redox potentials of the subclusters of the H-cluster, lowering activity, as shown in protein film electrochemistry (PFE). Together, these results indicate that H_oxH and its one-electron reduced counterpart H_red'H are artifacts of using a nonphysiological reductant, and not crucial catalytic intermediates. We propose renaming these states as the "dithionite (DT) inhibited" states H_ox-DT_i and H_red-DT_i. The broader potential implications of using a nonphysiological reductant in spectroscopic and mechanistic studies of enzymes are highlighted.

Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis

The activity of the reversible decarboxylase enzyme Fdc1 is dependent on prenylated FMN (prFMN), a recently discovered cofactor. The oxidized prFMN supports a 1,3-dipolar cycloaddition mechanism that underpins reversible decarboxylation. Fdc1 is a distinct member of the UbiD family of enzymes, with the canonical UbiD catalyzing the (de)carboxylation of para-hydroxybenzoic acid-type substrates. Here we show that the Escherichia coli UbiD enzyme, which is implicated in ubiquinone biosynthesis, cannot be isolated in an active holoenzyme form despite the fact active holoFdc1 is readily obtained. Formation of holoUbiD requires reconstitution in vitro of the apoUbiD with reduced prFMN. Furthermore, although the Fdc1 apoenzyme can be readily reconstituted and activated, in vitro oxidation to the mature prFMN cofactor stalls at formation of a radical prFMN species in holoUbiD. Further oxidative maturation in vitro occurs only at alkaline pH, suggesting a proton-coupled electron transfer precedes formation of the fully oxidized prFMN. Crystal structures of holoUbiD reveal a relatively open active site potentially occluded from solvent through domain motion. The presence of a prFMN sulfite-adduct in one of the UbiD crystal structures confirms oxidative maturation does occur at ambient pH on a slow time scale. Activity could not be detected for a range of putative para-hydroxybenzoic acid substrates tested. However, the lack of an obvious hydrophobic binding pocket for the octaprenyl tail of the proposed ubiquinone precursor substrate does suggest UbiD might act on a non-prenylated precursor. Our data reveals an unexpected variation occurs in domain mobility, prFMN binding, and maturation by the UbiD enzyme family.

Identity of the emitter in the bacterial luciferase luminescence reaction: binding and fluorescence quantum yield studies of 5-decyl-4a-hydroxy-4a,5-dihydroriboflavin-5'-phosphate as a model

The excited state of 4a-hydroxy-4a,5-dihydroFMN has been postulated to be the emitter in the bacterial bioluminescence reaction. However, while the bioluminescence quantum yield of the luciferase emitter is about 0.16, chemiluminescence and fluorescence quantum yields of earlier flavin models mimicking the luciferase emitter were no more than 10(-5). To further examine the proposed chemical identity of the luciferase emitter, 5-decyl-4a-hydroxy-4a,5-dihydroFMN was prepared as a new flavin model. Both the wild-type Vibrio harveyi luciferase and a catalytically active alphaC106A mutant formed complexes with the flavin model at a 1:1 molar ratio with K(d) values at 2.4 and 1.2 microM, respectively. This flavin model inhibited the activity of both luciferases, suggesting that it was bound to the enzyme active center. While the free flavin model was itself only very weakly fluorescent, its binding to either luciferase species resulted in markedly enhanced fluorescence, peaking at 440 nm. The fluorescence quantum yields of 5-decyl-4a-hydroxy-4a,5-dihydroFMN bound to wild-type and alphaC106A luciferases were 0.08 and 0.05, respectively, which are about 50% of the respective emitter bioluminescence quantum yields of these two luciferases. The present findings clearly demonstrated that the luciferase active site was suitable for marked enhancement of fluorescence of 4a-hydroxyflavin and, hence, provides a strong support to the proposed identity of 4a-hydroxy-4a,5-dihydroFMN, in its exited state, as the luciferase emitter.

Characterization of the binding of Photobacterium phosphoreum P-flavin by Vibrio harveyi Luciferase

The isolated Photobacterium phosphoreum luciferase is associated with a bound flavin designated P-flavin and tentatively identified as 6-(3"-myristic acid)-FMN. Since FMN and myristic acid are products of the normal luciferase reaction, we explored the possibility that P-flavin can also be bound by luciferase from other luminous bacteria and serve as an active site probe. P-flavin has never been detected in Vibrio harveyi cells. We found that the V. harveyi luciferase binds P. phosphoreum P-flavin, at a ratio of 1 P-flavin per luciferase alphabeta dimer, and with concomitant absorption spectral perturbation of P-flavin, fluorescence quenching of P-flavin and luciferase, and activity inhibition of luciferase. Isolated P-flavin can be fully reduced photochemically. V. harveyi luciferase bound the oxidized P-flavin with a K(d) (or K(i) competitively against decanal) of 0.1-0.16 microM, which is three orders of magnitude lower than the K(d) for FMN binding but similar to that of reduced FMN binding. The reduced P-flavin exhibited a K(i) (competitively against the reduced FMN substrate) of 0.16 microM, also similar to the K(d) for reduced FMN. Hence, the covalent attachment of myristic acid to FMN greatly and preferentially enhanced the binding of oxidized P-flavin. The dissociation of P-flavin was slow in comparison with the binding of reduced FMN and decanal substrates. Modification of the alphaCys106 near the active site by N-ethylmaleimide can be retarded by P-flavin. These findings indicate that P-flavin is potentially a superb active site probe for luciferase. We hypothesize that P-flavin is a by-product of luciferase generated by a side reaction which is trivial with the V. harveyi luciferase but significant in the P. phosphoreum luciferase-catalyzed reaction.

A new reducing agent of flavins and its application to the assay of bacterial luciferase

Copper(I) plus ethylenediaminetetraacetic acid, Cu(I)-EDTA, reduces flavins. Using Cu(I)-EDTA reduction of riboflavin 5'-phosphate, a new assay method for bacterial luciferase is established. In previous assay methods, flavin and aldehyde substrates for luciferase have been routinely added to luciferase at different times; the new assay permits aldehyde and Cu(I)-reduced flavin to be injected simultaneously into air-saturated buffer containing luciferase. In the new assay method using Cu(I), bovine serum albumin is not required, the initial emission intensity is more than twice and the overall yield is about twice of that in the so-called standard assay for luciferase.

Electrochemical superoxidation of flavins: generation of active precursors in luminescent model systems

Using 3-methyllumiflavin and tetraacetyliriboflavin as examples, we have shown that the socalled "fully oxidized" flavins can be "superoxidized" at an anodic potential of 1.8 to 1.9 V giving flavin radical cation transients which are rapidly transformed in subsequent chemical reactions. An attack by H2O subsequent to the superoxidation of 3-methyllumiflavin provides a route for the formation of 4a-hydroxy-3-methyllumiflavin radical cation, as evident from the subsequent decomposition to the protonated form of the starting flavin. When 3-methyllumiflavin is superoxidized in the presence of a base, a recycling process occurs, allowing superoxidized flavin to be trapped in a slower, competitive conversion. The relatively more stable trapped product is active in reacting with H2O2 to emit chemiluminescence. Electrochemical oxidation of H2O2 in acetonitrile at 1.30 V in the presence of an oxidized flavin results in a direct protonation of the flavin by H+ generated from the electrolysis of H2O2. Minor reactions presumably provide alternative formations of the 4a-hydroperoxy- and 4a-hydroxy-flavin radical cation transients by the direct addition of HOO. and HO. radicals, which also arise in the oxidation of H2O2, to protonated flavin. Under such conditions the superoxidized flavin radical cation is apparently also formed, either directly or by process(es) such as decomposition of the flavin 4a-adduct radical cations. Subsequent reductions of either the superoxidized flavin or the flavin 4a-adduct radical cations lead to an almost steady level of luminescence.(ABSTRACT TRUNCATED AT 250 WORDS)