The dyad of the Y-junction- and a flavin module unites diverse redox enzymes.

The concomitant presence of two distinctive polypeptide modules, which we have chosen to denominate as the "Y-junction" and the "flavin" module, is observed in 3D structures of enzymes as functionally diverse as complex I, NAD(P)-dependent [NiFe]-hydrogenases and NAD(P)-dependent formate dehydrogenases. Amino acid sequence conservation furthermore suggests that both modules are also part of NAD(P)-dependent [FeFe]-hydrogenases for which no 3D structure model is available yet. The flavin module harbours the site of interaction with the substrate NAD(P) which exchanges two electrons with a strictly conserved flavin moiety. The Y-junction module typically contains four iron-sulphur centres arranged to form a Y-shaped electron transfer conduit and mediates electron transfer between the flavin module and the catalytic units of the respective enzymes. The Y-junction module represents an electron transfer hub with three potential electron entry/exit sites. The pattern of specific redox centres present both in the Y-junction and the flavin module is correlated to present knowledge of these enzymes' functional properties. We have searched publicly accessible genomes for gene clusters containing both the Y-junction and the flavin module to assemble a comprehensive picture of the diversity of enzymes harbouring this dyad of modules and to reconstruct their phylogenetic relationships. These analyses indicate the presence of the dyad already in the last universal common ancestor and the emergence of complex I's EFG-module out of a subgroup of NAD(P)- dependent formate dehydrogenases.

Mechanism of O2 diffusion and reduction in FeFe hydrogenases.

FeFe hydrogenases are the most efficient H2-producing enzymes. However, inactivation by O2 remains an obstacle that prevents them being used in many biotechnological devices. Here, we combine electrochemistry, site-directed mutagenesis, molecular dynamics and quantum chemical calculations to uncover the molecular mechanism of O2 diffusion within the enzyme and its reactions at the active site. We propose that the partial reversibility of the reaction with O2 results from the four-electron reduction of O2 to water. The third electron/proton transfer step is the bottleneck for water production, competing with formation of a highly reactive OH radical and hydroxylated cysteine. The rapid delivery of electrons and protons to the active site is therefore crucial to prevent the accumulation of these aggressive species during prolonged O2 exposure. These findings should provide important clues for the design of hydrogenase mutants with increased resistance to oxidative damage.

Does the environment around the H-cluster allow coordination of the pendant amine to the catalytic iron center in [FeFe] hydrogenases? Answers from theory.

[FeFe] hydrogenases are H2-evolving enzymes that feature a diiron cluster in their active site (the [2Fe]H cluster). One of the iron atoms has a vacant coordination site that directly interacts with H2, thus favoring its splitting in cooperation with the secondary amine group of a neighboring, flexible azadithiolate ligand. The vacant site is also the primary target of the inhibitor O2. The [2Fe]H cluster can span various redox states. The active-ready form (Hox) attains the Fe(II)Fe(I) state. States more oxidized than Hox were shown to be inactive and/or resistant to O2. In this work, we used density functional theory to evaluate whether azadithiolate-to-iron coordination is involved in oxidative inhibition and protection against O2, a hypothesis supported by recent results on biomimetic compounds. Our study shows that Fe-N(azadithiolate) bond formation is favored for an Fe(II)Fe(II) active-site model which disregards explicit treatment of the surrounding protein matrix, in line with the case of the corresponding Fe(II)Fe(II) synthetic system. However, the study of density functional theory models with explicit inclusion of the amino acid environment around the [2Fe]H cluster indicates that the protein matrix prevents the formation of such a bond. Our results suggest that mechanisms other than the binding of the azadithiolate nitrogen protect the active site from oxygen in the so-called H ox (inact) state.

Trinuclear terpyridine frustrated spin system with a Mn(IV)3O4 core: synthesis, physical characterization, and quantum chemical modeling of its magnetic properties.

The trinuclear oxo bridged manganese cluster, [Mn(IV)(3)O(4)(terpy)(terpyO(2))(2)(H(2)O)](S(2)O(8))(2) (5) (terpy = 2,2':2'',6'-terpyridine and terpyO(2) = 2,2':2'',6'-terpyridine 1,1''-dioxide), was isolated in an acidic aqueous medium from the reaction of MnSO(4), terpy, and oxone as chemical oxidant. The terpyO(2) ligands were generated in situ during the synthesis by partial oxidation of terpy. The complex crystallizes in the monoclinic space group P21/n with a = 14.251(5) A, b = 15.245(5) A, c = 24.672(5) A, alpha = 90.000(5) degrees, beta = 92.045(5) degrees, gamma = 90.000(5) degrees, and Z = 4. The triangular {Mn(IV)(3)O(4)}(4+) core observed in this complex is built up of a basal Mn(mu-O)(2)Mn unit where each Mn ion is linked to an apical Mn ion via mono(mu-O) bridges. The facial coordination of the two tridentate terpyO(2) ligands to the Mn(mu-O)(2)Mn unit allows the formation of the triangular core. 5 is also the first structurally characterized Mn complex with polypyridinyl N-oxide ligands. The variable-temperature magnetic susceptibility data for this complex, in the range of 10-300 K, are consistent with an S = 1/2 ground state and were fit using the spin Hamiltonian H(eff) with S(1) = S(2) = S(3) = 3/2, J(a) = -37 (+/-0.5) and J(b) = -53 (+/-1) cm(-1), where J(a) and J(b) are exchange constants through the mono-mu-oxo and the di-mu-oxo bridges, respectively. The doublet ground spin state of 5 is confirmed by EPR spectroscopic measurements. Density functional theory (DFT) calculations based on the broken symmetry approach reproduce the magnetic properties of 5 very well (calculated values: J(a) = -39.4 and J(b) = -55.9 cm(-1)), thus confirming the capability of this quantum chemical method for predicting the magnetic behavior of clusters involving more than two metal ions. The nature of the ground spin state of the magnetic {Mn(IV)(3)O(4)}(4+) core and the role of ancillary ligands on the magnitude of J are also discussed.