Adenosylmethionine-dependent iron-sulfur enzymes: versatile clusters in a radical new role.

Iron-sulfur clusters are widespread in biological systems and participate in a broad range of functions. These functions include electron transport, mediation of redox as well as non-redox catalysis, and regulation of gene expression. A new role for iron-sulfur clusters has emerged in recent years as a number of enzymes have been identified that utilize Fe-S clusters and S-adenosylmethionine (AdoMet) to initiate radical catalysis. This Fe-S cluster-mediated radical catalysis includes the generation of stable protein-centered radicals as well as generation of substrate radical intermediates, with evidence suggesting a common mechanism involving an intermediate adenosyl radical. Although the mechanism of generation of the adenosyl radical intermediate is currently not well understood, it likely represents novel chemistry for iron-sulfur clusters. The purpose of this review is to present the current state of knowledge of this newly emerging group of Fe-S/AdoMet enzymes.

Escherichia coli LipA is a lipoyl synthase: in vitro biosynthesis of lipoylated pyruvate dehydrogenase complex from octanoyl-acyl carrier protein.

The Escherichia coli lipA gene product has been genetically linked to carbon-sulfur bond formation in lipoic acid biosynthesis [Vanden Boom, T. J., Reed, K. E., and Cronan, J. E., Jr. (1991) J. Bacteriol. 173, 6411-6420], although in vitro lipoate biosynthesis with LipA has never been observed. In this study, the lipA gene and a hexahistidine tagged lipA construct (LipA-His) were overexpressed in E. coli as soluble proteins. The proteins were purified as a mixture of monomeric and dimeric species that contain approximately four iron atoms per LipA polypeptide and a similar amount of acid-labile sulfide. Electron paramagnetic resonance and electronic absorbance spectroscopy indicate that the proteins contain a mixture of [3Fe-4S] and [4Fe-4S] cluster states. Reduction with sodium dithionite results in small quantities of an S = 1/2 [4Fe-4S](1+) cluster with the majority of the protein containing a species consistent with an S = 0 [4Fe-4S](2+) cluster. LipA was assayed for lipoate or lipoyl-ACP formation using E. coli lipoate-protein ligase A (LplA) or lipoyl-[acyl-carrier-protein]-protein-N-lipoyltransferase (LipB), respectively, to lipoylate apo-pyruvate dehydrogenase complex (apo-PDC) [Jordan, S. W., and Cronan, J. E. (1997) Methods Enzymol. 279, 176-183]. When sodium dithionite-reduced LipA was incubated with octanoyl-ACP, LipB, apo-PDC, and S-adenosyl methionine (AdoMet), lipoylated PDC was formed. As shown by this assay, octanoic acid is not a substrate for LipA. Confirmation that LipA catalyzes formation of lipoyl groups from octanoyl-ACP was obtained by MALDI mass spectrometry of a recombinant PDC lipoyl-binding domain that had been lipoylated in a LipA reaction. These results provide information about the mechanism of LipA catalysis and place LipA within the family of iron-sulfur proteins that utilize AdoMet for radical-based chemistry.

Pyruvate formate-lyase-activating enzyme: strictly anaerobic isolation yields active enzyme containing a [3Fe-4S](+) cluster.

Pyruvate formate-lyase-activating enzyme (PFL-AE) from Escherichia coli (E. coli) catalyzes the stereospecific abstraction of a hydrogen atom from Gly734 of pyruvate formate-lyase (PFL) in a reaction that is strictly dependent on the cosubstrate S-adenosyl-l-methionine (AdoMet). Although PFL-AE is an iron-dependent enzyme, isolation of the enzyme with its metal center intact has proven difficult due to the oxygen sensitivity and lability of the metal center. We report here the first isolation of PFL-AE under nondenaturing, strictly anaerobic conditions. Iron and sulfide analysis as well as UV-visible, EPR, and resonance Raman data support the presence of a [3Fe-4S](+) cluster in the purified enzyme. The isolated native enzyme, but not apo-enzyme, exhibits a high specific activity (31 U/mg) in the absence of added iron, indicating that the native cluster is necessary and sufficient for enzymatic activity.

Catechol dioxygenases.

Catechol dioxygenases are key enzymes in the metabolism of aromatic rings by soil bacteria. Catechol dioxygenases have been found that participate in the metabolism of halogenated aromatic compounds and, in doing so, play a key role in bioremediation of halogenated pollutants. The catechol dioxygenases can be divided into two major groups: those that cleave the aromatic ring between the vicinal diols (the intradiol enzymes) and those that cleave the ring to one side of the vicinal diols (the extradiol enzymes). Whereas both types of catechol dioxygenase contain an active-site iron that is required absolutely for enzymic activity, the intradiol enzymes contain Fe(III), while the extradiol enzymes contain Fe(II). The nature of the protein ligands determines this specificity. The differences in oxidation state of the active-site iron appear to result in mechanistic differences that lead to the differing regioselectivity of the two groups of catechol dioxygenase. Mechanistic proposals based on available evidence suggest a substrate-activation mechanism for the intradiol enzymes and an oxygen-activation mechanism for the extradiol enzymes.

Evidence for retention of biological activity of a non-heme iron enzyme adsorbed on a silver colloid: a surface-enhanced resonance Raman scattering study.

The structure and catalytic properties of the enzyme (E) chlorocatechol dioxygenase (CCD) adsorbed on a citrate-reduced silver colloid are analyzed by surface-enhanced resonance Raman spectroscopy (SERRS). This is the first SERRS study of a non-heme metalloenzyme. It is demonstrated that the native conformation of CCD is retained in the adsorbed state by comparison of resonance Raman scattering (RRS) from CCD in solution with SERRS from CCD adsorbed on the silver colloid. Both spectra show clear evidence of vibrational bands typical of iron-tyrosinate proteins. Furthermore, it is demonstrated that adsorbed CCD retains 60-85% of its enzymatic activity in the reaction of catechol substrate (S) with O2 to give the dioxygenated product (P) cis,cis-muconate. This is accomplished by enzyme assays of Ag-adsorbed CCD and comparison of the SERRS of Ag-adsorbed enzyme-substrate (ES) complex under anaerobic conditions with that of Ag-adsorbed ES in the presence of dioxygen. The SERRS difference spectrum, ES(aerobic)--ES(anaerobic), shows clear evidence for the appearance of the vibrational modes of adsorbed product. The analogous SERR difference spectroscopy experiment is also carried out for the enzyme-inhibitor (EI) complex of CCD with tetrachlorocatechol (TCC). Slow turnover of CCD-TCC is observed by SERRS on exposure to dioxygen which is consistent with the slow rate of turnover of TCC by CCD in solution.

Overproduction, purification, and characterization of chlorocatechol dioxygenase, a non-heme iron dioxygenase with broad substrate tolerance.

We show here that purified chlorocatechol dioxygenase from Pseudomonas putida is able to oxygenate a wide range of substituted catechols with turnover numbers ranging from 2 to 29 s-1. This enzyme efficiently cleaves substituted catechols bearing electron-donating or multiple electron-withdrawing groups in an intradiol manner with kcat/KM values between 0.2 x 10(7) and 1.4 x 10(7) M-1 s-1. These unique catalytic properties prompted a comparison with the related but highly specific enzymes catechol 1,2-dioxygenase and protocatechuate 3,4-dioxygenase. The chlorocatechol dioxygenase gene (clcA) from the Pseudomonas plasmid pAC27 was subcloned into the expression vector pKK223-3, allowing production of chlorocatechol dioxygenase to approximately 7-8% of total cellular protein. An average of 4 mg of purified enzyme has been obtained per gram of wet cells. Protein and iron analyses indicate an iron stoichiometry of 1 iron/57.5-kDa homodimer, alpha 2Fe. The electronic absorption spectrum contains a broad tyrosinate to iron charge transfer transition centered at 430 nm (epsilon = 3095 M-1 cm-1 based on iron concentration) which shifts to 490 nm (epsilon = 3380 M-1 cm-1) upon catechol binding. The resonance Raman spectrum of the native enzyme exhibits characteristic tyrosine ring vibrations. Electron paramagnetic resonance data for the resting enzyme (g = 4.25, 9.83) is consistent with high-spin iron (III) in a rhombic environment. This similarity between the spectroscopic properties of the Fe(III) centers in chlorocatechol dioxygenase and the more specific dioxygenases suggests a highly conserved catalytic site. We infer that the unique catalytic properties of chlorocatechol dioxygenase are due to other characteristics of its substrate binding pocket.