A Water-Bridged H-Bonding Network Contributes to the Catalysis of the SAM-Dependent C-Methyltransferase HcgC

[Fe]-hydrogenase hosts an iron-guanylylpyridinol (FeGP) cofactor. The FeGP cofactor contains a pyridinol ring substituted with GMP, two methyl groups, and an acylmethyl group. HcgC, an enzyme involved in FeGP biosynthesis, catalyzes methyl transfer from S-adenosylmethionine (SAM) to C3 of 6-carboxymethyl-5-methyl-4-hydroxy-2-pyridinol (2). We report on the ternary structure of HcgC/S-adenosylhomocysteine (SAH, the demethylated product of SAM) and 2 at 1.7 angstrom resolution. The proximity of C3 of substrate 2 and the S atom of SAH indicates a catalytically productive geometry. The hydroxy and carboxy groups of substrate 2 are hydrogen-bonded with I115 and T179, as well as through a series of water molecules linked with polar and a few protonatable groups. These interactions stabilize the deprotonated state of the hydroxy groups and a keto form of substrate 2, through which the nucleophilicity of C3 is increased by resonance effects. Complemented by mutational analysis, a structure-based catalytic mechanism was proposed

Reconstitution of [Fe]-hydrogenase using model complexes

[Fe]-Hydrogenase catalyses the reversible hydrogenation of a methenyltetrahydromethanopterin substrate, which is an intermediate step during the methanogenesis from CO2 and H-2. The active site contains an iron-guanylylpyridinol cofactor, in which Fe2+ is coordinated by two CO ligands, as well as an acyl carbon atom and a pyridinyl nitrogen atom from a 3,4,5,6-substituted 2-pyridinol ligand. However, the mechanism of H-2 activation by [Fe]-hydrogenase is unclear. Here we report the reconstitution of [Fe]-hydrogenase from an apoenzyme using two FeGP cofactor mimics to create semisynthetic enzymes. The small-molecule mimics reproduce the ligand environment of the active site, but are inactive towards H-2 binding and activation on their own. We show that reconstituting the enzyme using a mimic that contains a 2-hydroxypyridine group restores activity, whereas an analogous enzyme with a 2-methoxypyridine complex was essentially inactive. These findings, together with density functional theory computations, support a mechanism in which the 2-hydroxy group is deprotonated before it serves as an internal base for heterolytic H-2 cleavage

The exchange activities of [Fe] hydrogenase (iron–sulfur-cluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases

[Fe] hydrogenase (iron–sulfur-cluster-free hydrogenase) catalyzes the reversible reduction of methenyltetrahydromethanopterin (methenyl-H4MPT+) with H2 to methylene-H4MPT, a reaction involved in methanogenesis from H2 and CO2 in many methanogenic archaea. The enzyme harbors an iron-containing cofactor, in which a low-spin iron is complexed by a pyridone, two CO and a cysteine sulfur. [Fe] hydrogenase is thus similar to [NiFe] and [FeFe] hydrogenases, in which a low-spin iron carbonyl complex, albeit in a dinuclear metal center, is also involved in H2 activation. Like the [NiFe] and [FeFe] hydrogenases, [Fe] hydrogenase catalyzes an active exchange of H2 with protons of water; however, this activity is dependent on the presence of the hydride-accepting methenyl-H4MPT+. In its absence the exchange activity is only 0.01% of that in its presence. The residual activity has been attributed to the presence of traces of methenyl-H4MPT+ in the enzyme preparations, but it could also reflect a weak binding of H2 to the iron in the absence of methenyl-H4MPT+. To test this we reinvestigated the exchange activity with [Fe] hydrogenase reconstituted from apoprotein heterologously produced in Escherichia coli and highly purified iron-containing cofactor and found that in the absence of added methenyl-H4MPT+ the exchange activity was below the detection limit of the tritium method employed (0.1 nmol min−1 mg−1). The finding reiterates that for H2 activation by [Fe] hydrogenase the presence of the hydride-accepting methenyl-H4MPT+ is essentially required. This differentiates [Fe] hydrogenase from [FeFe] and [NiFe] hydrogenases, which actively catalyze H2/H2O exchange in the absence of exogenous electron acceptors

Charakterisierung der an der Biosynthese des Cofaktors der [Fe]-Hydrogenase Hmd beteiligten Hcg-Proteine

[Fe]-hydrogenase (Hmd) catalyzes the reduction of methenyl-H4MPT+ to methylene-H4MPT using H2 as electron donor in the hydrogenotrophic methanogenic pathway. The production of Hmd was upregulated when the cell was grown under Ni-limiting environment. Hmd is composed of homodimer; the active sites are located at the cleft formed by the N-terminal domain and central domain. The N-terminal domain binds an iron-guanylylpyridinol (FeGP) cofactor, which is prosthetic group of this enzyme. The FeGP cofactor is composed of a low spin FeII ligated with two CO, an acyl-C and pyridinol-N; in addition, Cys-S and a solvent are bound to the iron site in the enzyme. The pyridinol ring is substituted with GMP moiety and two methyl groups. Genome analysis indicated that there are seven conserved genes which is named hcg gene cluster containing hcgAG and hmd genes. Therefore, it was predicted that the hcg cluster is responsible for biosynthesis of the FeGP cofactor. From the hcg genes sequences, we could not deduce the function of the proteins. However, using the “structure to function” strategy and biochemical assays, we could identify the function of some Hcg proteins. In this thesis, I describe the function of HcgC based on crystal structure and biochemical analyses. The isotope-labeling experiment indicated that the C3 methyl group comes from methionine, probably via S-adenosylmethionine (SAM). Structure comparisons of HcgC with other proteins suggested similarity of HcgC to SAM-dependent methyltransferases. Co-crystallization of HcgC and SAM revealed that SAM binds to the active site of HcgC. Docking simulation with a possible methyl-acceptor pyridinol suggested that the binding site of the pyridinol. The predicted substrate pyridinol was chemically synthesized and the enzyme activity was determined. The structure of the HcgC-reaction product was determined by NMR, which confirmed that HcgC transfer the methyl group from SAM to C3 of pyridinol. In order to analyze the catalytic mechanism of HcgC, co-crystallizaiton of HcgC, pyridinol, SAM or SAH was performed. The substrate binding site structure showed that seven water molecules connected pyridinol to protein. The only interaction of pyridinol with amino acid side chain was Thr179-OH. The C3 of pyridinol was close to the sulfur of SAH. In the crystal structure, there was no amino acid, which functions as general base of the typical methyl-transfer reaction. We proposed that the water molecules stabilize the deprotonated form of pyridinol by resonance effect, which increases the nucleophilicity of C3. Mutation analysis supported the essential contribution of the water molecules

Catabolic Pathways and Enzymes Involved in Anaerobic Methane Oxidation

# Springer International Publishing AG 2017 M. Boll (ed.), Anaerobic Utilization of Hydrocarbons, Oils, and Lipids, Handbook of Hydrocarbon and Lipid Microbiology, DOI 10.1007/978-3-319-33598-8_3-1Microbes use two distinct catabolic pathways for life with the fuel methane: aerobic methane oxidation carried out by bacteria and anaerobic methane oxidation carried out by archaea. The archaea capable of anaerobic oxidation of methane, anaerobic methanotrophs (ANME), are phylogenetically related to methanogens. While the carbon metabolism in ANME follows the pathway of reverse methanogenesis, the mode of electron transfer from methane oxidation to the terminal oxidant is remarkably versatile. This chapter discusses the catabolic pathways of methane oxidation coupled to the reduction of nitrate, sulfate, and metal oxides. Methane oxidation with sulfate and metal oxides are hypothesized to involve direct interspecies electron transfer and extracellular electron transfer. Cultivation of ANME, their mechanisms of energy conservation, and details about the electron transfer pathways to the ultimate oxidants are rather new and quickly developing research fields, which may reveal novel metabolisms and redox reactions. The second section focuses on the carbon catabolism from methane to CO2 and the biochemistry in ANME with its unique enzymes containing Fe, Ni, Co, Mo, and W that are compared with their homologues found in methanogens.Peer reviewe

Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites

Methylotrophy, the ability of microorganisms to grow on reduced one-carbon substrates such as methane or methanol, is a feature of various bacterial species. The prevailing oxidation pathway depends on tetrahydromethanopterin (H4MPT) and methylofuran (MYFR), an analog of methanofuran from methanogenic archaea. Formyltransferase/hydrolase complex (Fhc) generates formate from formyl-H4MPT in two consecutive reactions where MYFR acts as a carrier of one-carbon units. Recently, we chemically characterized MYFR from the model methylotroph Methylorubrum extorquens and identified an unusually long polyglutamate side chain of up to 24 glutamates. Here, we report on the crystal structure of Fhc to investigate the function of the polyglutamate side chain in MYFR and the relatedness of the enzyme complex with the orthologous enzymes in archaea. We identified MYFR as a prosthetic group that is tightly, but noncovalently, bound to Fhc. Surprisingly, the structure of Fhc together with MYFR revealed that the polyglutamate side chain of MYFR is branched and contains glutamates with amide bonds at both their α- and γ-carboxyl groups. This negatively charged and branched polyglutamate side chain interacts with a cluster of conserved positively charged residues of Fhc, allowing for strong interactions. The MYFR binding site is located equidistantly from the active site of the formyltransferase (FhcD) and metallo-hydrolase (FhcA). The polyglutamate serves therefore an additional function as a swinging linker to shuttle the one-carbon carrying amine between the two active sites, thereby likely increasing overall catalysis while decreasing the need for high intracellular MYFR concentrations.ISSN:0027-8424ISSN:1091-649

Krypton-derivatization highlights O 2 -channeling in a four-electron reducing oxidase

International audienceF420H2-oxidase (FprA) catalyses the four-electron reduction of O2 to 2H2O using the reduced form of F420 as electron donor. The hydrophobic O2-channel detected by Kr-derivatization and the concerted movement of a gating loop could contribute to prevent unwanted side-reaction between the catalytic intermediates and solvents, therefore preventing reactive oxygen species formation