Evert C. Duin

LytB protein catalyzes the terminal step of the 2‐C‐methyl‐D‐erythritol‐4‐phosphate pathway of isoprenoid biosynthesis

Recombinant LytB protein from the thermophilic eubacterium Aquifex aeolicus produced in Escherichia coli was purified to apparent homogeneity. The purified LytB protein catalyzed the reduction of (E)‐4‐hydroxy‐3‐methyl‐but‐2‐enyl diphosphate (HMBPP) in a defined in vitro system. The reaction products were identified as isopentenyl diphosphate and dimethylallyl diphosphate. A spectrophotometric assay was established to determine the steady‐state kinetic parameters of LytB protein. The maximal specific activity of 6.6±0.3 μmol min−1 mg−1 protein was determined at pH 7.5 and 60°C. The k cat value of the LytB protein was 3.7±0.2 s−1 and the K m value for HMBPP was 590±60 μM.

Functional characterization of GcpE, an essential enzyme of the non‐mevalonate pathway of isoprenoid biosynthesis

The gcpE gene product controls one of the terminal steps of isoprenoid biosynthesis via the mevalonate independent 2‐C‐methyl‐D‐erythritol‐4‐phosphate (MEP) pathway. This pathway is utilized by a variety of eubacteria, the plastids of algae and higher plants, and the plastid‐like organelle of malaria parasites. Recombinant GcpE protein from the hyperthermophilic bacterium Thermus thermophilus was produced in Escherichia coli and purified under dioxygen‐free conditions. The protein was enzymatically active in converting 2‐C‐methyl‐D‐erythritol‐2,4‐cyclodiphosphate (MEcPP) into (E)‐4‐hydroxy‐3‐methyl‐but‐2‐enyl diphosphate (HMBPP) in the presence of dithionite as reductant. The maximal specific activity was 0.6 μmol min−1 mg−1 at pH 7.5 and 55°C. The k cat value was 0.4 s−1 and the K m value for HMBPP 0.42 mM.

Structure of (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, the terminal enzyme of the non-mevalonate pathway.

Molecular evolution has evolved two metabolic routes for isoprenoid biosynthesis: the mevalonate and the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway. The MEP pathway is used by most pathogenic bacteria and some parasitic protozoa (including the malaria parasite, Plasmodium falciparum) as well as by plants, but is not present in animals. The terminal reaction of the MEP pathway is catalyzed by (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) reductase (LytB), an enzyme that converts HMBPP into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Here, we present the structure of Aquifex aeolicus LytB, at 1.65 A resolution. The protein adopts a cloverleaf or trefoil-like structure with each monomer in the dimer containing three alpha/beta domains surrounding a central [Fe3S4] cluster ligated to Cys13, Cys96, and Cys193. Two highly conserved His (His 42 and His 124) and a totally conserved Glu (Glu126) are located in the same central site and are proposed to be involved in ligand binding and catalysis. Substrate access is proposed to occur from the front-side face of the protein, with the HMBPP diphosphate binding to the two His and the 4OH of HMBPP binding to the fourth iron thought to be present in activated clusters, while Glu126 provides the protons required for IPP/DMAPP formation.

Determination of kinetic parameters, Km and kcat, with a single experiment on a chip.

We have demonstrated a multistep enzyme reaction on a chip to determine the key kinetic parameters of enzyme reaction. We designed and fabricated a fully integrated microfluidic chip to have sample metering, mixing, and incubation functionalities. The chip generates a gradient of reagent concentrations in 11 parallel processors. We used beta-galactosidase and its substrate, resorufin-beta-D-galactopyranoside, as the model system of the enzyme reaction. With a single experiment on the chip, we determined the key parameters for the enzyme kinetics, K(m) and k(cat), and evaluated the effect of inhibitor concentrations on the reaction rates. This study provides a new tool for evaluating various effectors, such as inhibitors and cofactors, on the initial rate of an enzyme reaction, and it could be applied to a comprehensive bio/chemical reaction study.

Biological and Synthetic [Fe3S4] Clusters

Publisher Summary The discovery and characterization of [Fe3S4] clusters is one of the classic stories in bioinorganic chemistry and an excellent case study for students new to this area. Particularly, it serves to demonstrate the power of a multidisciplinary approach incorporating X-ray crystallography, the full armory of biophysical spectroscopic methods, molecular biology, and synthetic inorganic chemistry. The class of Fe–S proteins, containing 3Fe clusters, was reviewed soon after their discovery and before the structure and physiological relevance had been definitively established. This chapter summarizes the current understanding of the structural, electronic, and redox properties of biological and synthetic [Fe3S4] and heterometallic [MFe3S4] clusters. This chapter emphasizes the relevance to structure–function relations of iron–sulfur clusters, in general, and the major unresolved issues concerning [Fe3S4] clusters.

Heterodisulfide reductase from Methanothermobacter marburgensis contains an active-site [4Fe-4S] cluster that is directly involved in mediating heterodisulfide reduction.

Heterodisulfide reductases (HDRs) from methanogenic archaea are iron–sulfur flavoproteins or hemoproteins that catalyze the reversible reduction of the heterodisulfide (CoM‐S–S‐CoB) of the methanogenic thiol coenzymes, coenzyme M (CoM‐SH) and coenzyme B (CoB‐SH). In this work, the ground‐ and excited‐state electronic properties of the paramagnetic Fe–S clusters in Methanothermobacter marburgensis HDR have been characterized using the combination of electron paramagnetic resonance and variable‐temperature magnetic circular dichroism spectroscopies. The results confirm multiple S=1/2 [4Fe–4S]+ clusters in dithionite‐reduced HDR and reveal spectroscopically distinct S=1/2 [4Fe–4S]3+ clusters in oxidized HDR samples treated separately with the CoM‐SH and CoB‐SH cosubstrates. The active site of HDR is therefore shown to contain a [4Fe–4S] cluster that is directly involved in mediating heterodisulfide reduction. The catalytic mechanism of HDR is discussed in light of the crystallographic and spectroscopic studies of the related chloroplast ferredoxin:thioredoxin reductase class of disulfide reductases.

The nickel enzyme methyl-coenzyme M reductase from methanogenic archaea: in vitro interconversions among the EPR detectable MCR-red1 and MCR-red2 states.

Abstract. Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane from methyl-coenzyme M and coenzyme B in methanogenic archaea. The enzyme contains tightly bound the nickel porphinoid F430. The nickel enzyme has been shown to be active only when its prosthetic group is in the Ni(I) reduced state. In this state MCR exhibits the nickel-based EPR signal red1. We report here for the MCR from Methanothermobacter marburgensis that the EPR spectrum of the active enzyme changed upon addition or removal of coenzyme M, methyl coenzyme M and/or coenzyme B. In the presence of methyl-coenzyme M the red1 signal showed a more resolved 14N-superhyperfine splitting than in the presence of coenzyme M indicating a possible axial ligation of the substrate to the Ni(I). In the presence of methyl-coenzyme M and coenzyme B the red1 signal was the same as in the presence of methyl-coenzyme M alone. However, in the presence of coenzyme M and coenzyme B a highly rhombic EPR signal, MCR-red2, was induced, which was found to be light sensitive and appeared to be formed at the expense of the MCR-red1 signal. Upon addition of methyl-coenzyme M, the red2 signal disappeared and the red1 signal increased again. The red2 signal of MCR with 61Ni-labeled cofactor was significantly broadened indicating that the signal is nickel or nickel-ligand based.

Paramagnetic Intermediates of (E)-4-Hydroxy-3-methylbut-2-enyl Diphosphate Synthase (GcpE/IspG) under Steady-State and Pre-Steady-State Conditions

(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate synthase (GcpE/IspG) converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate (MEcPP) into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) in the penultimate step of the methyl-erythritol phosphate (MEP) pathway for isoprene biosynthesis. MEcPP is a cyclic compound and the reaction involves the opening of the ring and removal of the C3 hydroxyl group consuming a total of two electrons. The enzyme contains a single [4Fe-4S] cluster in its active site. Several paramagnetic species are observed in steady-state and pre-steady-state kinetic studies. The first signal detected is from a transient species that displays a rhombic electron paramagnetic resonance (EPR) signal with g(xyz) = 2.000, 2.019, and 2.087 (FeS(A)). A second set of EPR signals (FeS(B)) accumulated during the reaction. Labeling studies with (57)Fe showed that all species observed are iron-sulfur-based. (31)P-ENDOR measurements on the FeS(A) species showed a weak (31)P coupling which is in line with binding of the substrate to the enzyme in close proximity of the active-site cluster. On the basis of the EPR/ENDOR measurements, we propose a direct binding of the substrate to the [4Fe-4S] cluster during the reaction, and therefore that the iron-sulfur cluster is directly involved in a reductive elimination of a hydroxyl group. The FeS(B) signal also showed (31)P coupling; in this case, however, it could be shown that the signal is due to the binding of the reaction product HMBPP to the active site cluster.

Spectroscopic investigation of the nickel-containing porphinoid cofactor F 430 . Comparison of the free cofactor in the +1, +2 and +3 oxidation states with the cofactor bound to methyl-coenzyme M reductase in the silent, red and ox forms

Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea. It contains the nickel porphinoid F430, a prosthetic group that has been proposed to be directly involved in the catalytic cycle by the direct binding and subsequent reduction of the substrate methyl-coenzyme M. The active enzyme (MCRred1) can be generated in vivo and in vitro by reduction from MCRox1, which is an inactive form of the enzyme. Both the MCRred1 and MCRox1 forms have been proposed to contain F430 in the Ni(I) oxidation state on the basis of EPR and ENDOR data. In order to further address the oxidation state of the Ni center in F430, variable-temperature, variable-field magnetic circular dichroism (VTVH MCD), coupled with parallel absorption and EPR studies, have been used to compare the electronic and magnetic properties of MCRred1, MCRox1, and various EPR silent forms of MCR, with those of the isolated penta-methylated cofactor (F430M) in the +1, +2 and +3 oxidation states. The results confirm Ni(I) assignments for MCRred1 and MCRred2 forms of MCR and reveal charge transfer transitions involving the Ni d orbitals and the macrocycle π orbitals that are unique to Ni(I) forms of F430. Ligand field transitions associated with S=1 Ni(II) centers are assigned in the near-IR MCD spectra of MCRox1-silent and MCR-silent, and the splitting in the lowest energy d–d transition is shown to correlate qualitatively with assessments of the zero-field splitting parameters determined by analysis of VTVH MCD saturation magnetization data. The MCD studies also support rationalization of MCRox1 as a tetragonally compressed Ni(III) center with an axial thiolate ligand or a coupled Ni(II)-thiyl radical species, with the reality probably lying between these two extremes. The reinterpretation of MCRox1 as a formal Ni(III) species rather than an Ni(I) species obviates the need to invoke a two-electron reduction of the F430 macrocyclic ligand on reductive activation of MCRox1 to yield MCRred1.

Coordination and geometry of the nickel atom in active methyl-coenzyme M reductase from Methanothermobacter marburgensis as detected by X-ray absorption spectroscopy

Abstract. Methyl-coenzyme M reductase (MCR) catalyzes the reduction of methyl-coenzyme M (CH3–S–CoM) to methane. The enzyme contains as a prosthetic group the nickel porphinoid F430 which in the active enzyme is in the EPR-detectable Ni(I) oxidation state. Crystal structures of several inactive Ni(II) forms of the enzyme but not of the active Ni(I) form have been reported. To obtain structural information on the active enzyme–substrate complex we have now acquired X-ray absorption spectra of active MCR in the presence of either CH3–S–CoM or the substrate analog coenzyme M (HS–CoM). For both MCR complexes the results are indicative of the presence of a five-coordinate Ni(I), the five ligands assigned as four nitrogen ligands from F430 and one oxygen ligand. Analysis of the spectra did not require the presence of a sulfur ligand indicating that CH3–S–CoM and HS–CoM were not coordinated via their sulfur atom to nickel in detectable amounts. As a control, X-ray absorption spectra were evaluated of three enzymatically inactive MCR forms, MCR-silent, MCR-ox1-silent and MCR-ox1, in which the nickel is known to be six-coordinate. Comparison of the edge position of the X-ray absorption spectra revealed that the Ni(I) in the active enzyme is more reduced than the Ni in the two EPR-silent Ni(II) states. Surprisingly, the edge position of the EPR-active MCR-ox1 state was found to be the same as that of the two silent states indicating similar electron density on the nickel. Electronic supplementary material is available if you access this article at http://www.dx.doi.org/10.1007/s00775-002-0399-2. On that page (frame on the left side), a link takes you directly to the supplementary material.