Activation of the cytochrome cd1 nitrite reductase from Paracoccus pantotrophus. Reaction of oxidized enzyme with substrate drives a ligand switch at heme c

A mechanistic study of nitrite reduction on iron(ii) complexes of methylated N-confused porphyrins

Proton delivery to the prosthetic group is a crucial step to sustain the activity of nitrite reductase. An iron N-confused porphyrin (NCP) complex, which is capable of relaying protons from the outer pyrrolic nitrogen (N_out-H) of the inverted pyrrole ring to the axial coordinated ligand, has been demonstrated to facilitate facile nitrite reduction. Time-dependent FTIR studies on the reaction between [Fe^II(HCTPPMe)Br] (1) and a nitrite anion revealed a two-step process involving conversion of the starting complex 1 to an {Fe(NO)}⁷ intermediate, [Fe(CTPPMe)(NO)] (5), before the detection of [Fe(CTPPCH₂)(NO)] (3), an {Fe(NO)}⁶ end product. Moreover, spectroscopic data confirm that N_out-H on the NCP core is indispensable to the proceeding of the nitrite reduction reaction. Mass spectra have detected the coordination of a nitrite to the iron center while DFT theoretical calculations suggest that subsequent intramolecular proton transfer to a nitro group to form [Fe(CTPPMe)(HNO₂)] (6a) evokes a homolytic N-OH bond fission on axial nitrous acid due to an enhanced π-back-bonding to produce an {Fe(NO)}⁷ intermediate and to release a hydroxyl radical. The subsequent oxidation of an {Fe(NO)}⁷ intermediate by the hydroxyl radical gave the final product, {Fe(NO)}⁶ [Fe(CTPPCH₂)(NO)] (3). This study illustrates a proton assisted small molecule activation on the iron N-confused porphyrin coordination sphere and provides complemental insights into the mechanism of enzymatic nitrite reduction reactions.

Engineered holocytochrome c synthases that biosynthesize new cytochromes c

Cytochrome c (cyt c), required for electron transport in mitochondria, possesses a covalently attached heme cofactor. Attachment is catalyzed by holocytochrome c synthase (HCCS), leading to two thioether bonds between heme and a conserved CXXCH motif of cyt c In cyt c, histidine (His19) of CXXCH acts as an axial ligand to heme iron and upon release of holocytochrome c from HCCS, folding leads to formation of a second axial interaction with methionine (Met81). We previously discovered mutations in human HCCS that facilitate increased biosynthesis of cyt c in recombinant Escherichia coli Focusing on HCCS E159A, novel cyt c variants in quantities that are sufficient for biophysical analysis are biosynthesized. Cyt c H19M, the first bis-Met liganded cyt c, is compared with other axial ligand variants (M81A, M81H) and single thioether cyt c variants. For variants with axial ligand substitutions, electronic absorption, near-UV circular dichroism, and electron paramagnetic resonance spectroscopy provide evidence that axial ligands are changed and the heme environment is altered. Circular dichroism spectra in far UV and thermal denaturation analyses demonstrate that axial ligand changes do not affect secondary structures and stability. Redox potentials span a 400-mV range (+349 mV vs. standard hydrogen electrode, H19M; +252 mV, WT; -19 mV, M81A; -69 mV, M81H). We discuss the results in the context of a four-step mechanism for HCCS, whereby HCCS mutants such as E159A are enhanced in release (step 4) of cyt c from the HCCS active site; thus, we term these "release mutants."

The functional role of the structure of the dioxo-isobacteriochlorin in the catalytic site of cytochrome cd1 for the reduction of nitrite

Cytochrome cd1 is a key enzyme in bacterial denitrification and catalyzes one-electron reduction of nitrite (NO2-) to nitric oxide (NO) at the heme d1 center under anaerobic conditions. The heme d1 has a unique dioxo-isobacteriochlorin structure and is present only in cytochrome cd1. To reveal the functional role of the unique heme d1 in the catalytic nitrite reduction, we studied effect of the porphyrin macrocycle on each reaction step of the catalytic cycle of cytochrome cd1 using synthetic model complexes. The complexes investigated are iron complexes of dioxo-octaethylisobacteriochlorin (1), mono-oxo-octaethylchlorin (2) and octaethylporphyrin (3). We show here that the reduction potential for the transition from the ferric state to the ferrous state and the binding constant for binding of NO2- to the ferrous complex increases with a trend of 3 < 2 < 1. However, the reactivity of the ferrous nitrite complex with protons increases in the reversed order, 1 < 2 < 3. We also show that the iron bound NO of the ferric NO complex is readily replaced by addition of 1 equiv. of p-nitrophenolate. These results indicate that the dioxo-isobacteriochlorin structure is superior to porphyrin and mono-oxo-chlorin structures in the first iron reduction step, the second nitrite binding step, and the NO dissociation step, but inferior in the third nitrite reduction step. These results suggest that the heme d1 has evolved as the catalytic site of cytochrome cd1 to catalyze the nitrite reduction at the highest possible redox potential while maintaining its catalytic activity.

Solvent accessibility in the distal heme pocket of the nitrosyl d(1)-heme complex of Pseudomonas stutzeri cd(1) nitrite reductase

In nitrite reductase (cd(1) NIR), the c-heme mediates electron transfer to the catalytic d(1)-heme where nitrite (NO(2)(-)) is reduced to nitric oxide (NO). An interesting feature of this enzyme is the relative lability of the reaction product NO bound to the d(1)-heme. Marked differences in the c- to d(1)-heme electron-transfer rates were reported for cd(1) NIRs from different sources, such as Pseudomonas stutzeri (P. stutzeri) and Pseudomonas aeruginosa (P. aeruginosa). The three-dimensional structure of the P. aeruginosa enzyme has been determined, but that of the P. stutzeri enzyme is still unknown. The difference in electron transfer rates prompted a comparison of the structural properties of the d(1)-heme pocket of P. stutzeri cd(1) NIR with those of the P. aeruginosa wild type enzyme (WT) and its Y10F using their nitrosyl d(1)-heme complexes. We applied high field pulse electron paramagnetic resonance (EPR) techniques that detect nuclear spins in the close environment of the spin bearing Fe(II)-NO entity. We observed similarities in the rhombic g-tensor and detected a proximal histidine ligand with (14)N hyperfine and quadrupole interactions also similar to those of P. aeruginosa WT and Y10F mutant complexes. In contrast, we also observed significant differences in the H-bond network involving the NO ligand and a larger solvent accessibility for P. stutzeri attributed to the absence of this tyrosine residue. For P. aeruginosa, cd(1) NIR domain swapping allows Tyr(10) to become H-bonded to the bound NO substrate. These findings support a previous suggestion that the large difference in the c- to d(1)-heme electron transfer rates between the two enzymes is related to solvent accessibility of their d(1)-heme pockets.

Nitrite biosensing via selective enzymes--a long but promising route

The last decades have witnessed a steady increase of the social and political awareness for the need of monitoring and controlling environmental and industrial processes. In the case of nitrite ion, due to its potential toxicity for human health, the European Union has recently implemented a number of rules to restrict its level in drinking waters and food products. Although several analytical protocols have been proposed for nitrite quantification, none of them enable a reliable and quick analysis of complex samples. An alternative approach relies on the construction of biosensing devices using stable enzymes, with both high activity and specificity for nitrite. In this paper we review the current state-of-the-art in the field of electrochemical and optical biosensors using nitrite reducing enzymes as biorecognition elements and discuss the opportunities and challenges in this emerging market.

Review: studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis-histidine and histidine-methionine axial iron coordination

Six-coordinated heme groups are involved in a large variety of electron transfer reactions because of their ability to exist in both the ferrous (Fe(2+)) and ferric (Fe(3+)) state without any large differences in structure. Our studies on hemes coordinated by two histidines (bis-His) and hemes coordinated by histidine and methionine (His-Met) will be reviewed. In both of these coordination environments, the heme core can exhibit ferric low spin (electron paramagnetic resonance EPR) signals with large g(max) values (also called Type I, highly anisotropic low spin, or highly axial low spin, HALS species) as well as rhombic EPR (Type II) signals. In bis-His coordinated hemes rhombic and HALS envelopes are related to the orientation of the His groups with respect to each other such that (i) parallel His planes results in a rhombic signal and (ii) perpendicular His planes results in a HALS signal. Correlation between the structure of the heme and its ligands for heme with His-Met axial ligation and ligand-field parameters, as derived from a large series of cytochrome c variants, show, however, that for such a combination of axial ligands there is no clear-cut difference between the large g(max) and the "small g-anisotropy" cases as a result of the relative Met-His arrangements. Nonetheless, a new linear correlation links the average shift delta of the heme methyl groups with the g(max) values.

Formation of nitric oxide from nitrite by the ferriheme b protein nitrophorin 7

Recently, the conversion of nitrite into NO by certain heme proteins, in particular hemoglobin, gained much interest as a physiologically important source of NO in human tissue. However, in an aqueous environment, nitrite reduction at an iron porphyrin occurs either through oxidation of ferroheme to ferriheme or with the assistance of a second substrate molecule. Here we report on the reduction of nitrite in the absence of a second substrate at the heme center of the ferriheme protein nitrophorin 7 (NP7) resulting in the formation of NO and restoration of the ferriheme center. The product was spectroscopically characterized, in particular by resonance Raman and FT-IR spectroscopy. Performing the reaction in the presence of the NO trap 2-(4-trimethylammonio)phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (TMA-PTIO) revealed that continuous NO production is possible, i.e., that NP7 is fully restored upon a single turnover. Thus, NP7 is the first case of a b-type heme that performs reduction of nitrite as a single substrate out of the iron(III) state.

New insights into the activity of Pseudomonas aeruginosa cd1 nitrite reductase

The cytochrome cd(1) nitrite reductases are enzymes that catalyse the reduction of nitrite to nitric oxide (NO) in the bacterial energy conversion denitrification process. These enzymes contain two different redox centres: one covalently bound c-haem, which is reduced by external donors, and one peculiar d(1)-haem, where catalysis occurs. In the present paper, we summarize the current understanding of the reaction of nitrite reduction in the light of the most recent results on the enzyme from Pseudomonas aeruginosa and discuss the differences between enzymes from different organisms. We have evidence that release of NO from the ferrous d(1)-haem occurs rapidly enough to be fully compatible with the turnover, in contrast with previous hypotheses, and that the substrate nitrite is able to displace NO from the d(1)-haem iron. These results shed light on the mechanistic details of the activity of cd(1) nitrite reductases and on the biological role of the d(1)-haem, whose presence in this class of enzymes has to date been unexplained.

Modulation of the ligand-field anisotropy in a series of ferric low-spin cytochrome c mutants derived from Pseudomonas aeruginosa cytochrome c-551 and Nitrosomonas europaea cytochrome c-552: a nuclear magnetic resonance and electron paramagnetic resonance study

Cytochromes of the c type with histidine-methionine (His-Met) heme axial ligation play important roles in electron-transfer reactions and in enzymes. In this work, two series of cytochrome c mutants derived from Pseudomonas aeruginosa (Pa c-551) and from the ammonia-oxidizing bacterium Nitrosomonas europaea (Ne c-552) were engineered and overexpressed. In these proteins, point mutations were induced in a key residue (Asn64) near the Met axial ligand; these mutations have a considerable impact both on heme ligand-field strength and on the Met orientation and dynamics (fluxionality), as judged by low-temperature electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectra. Ne c-552 has a ferric low-spin (S = 1/2) EPR signal characterized by large g anisotropy with g(max) resonance at 3.34; a similar large g(max) value EPR signal is found in the mitochondrial complex III cytochrome c1. In Ne c-552, deletion of Asn64 (NeN64Delta) changes the heme ligand field from more axial to rhombic (small g anisotropy and g(max) at 3.13) and furthermore hinders the Met fluxionality present in the wild-type protein. In Pa c-551 (g(max) at 3.20), replacement of Asn64 with valine (PaN64V) induces a decrease in the axial strain (g(max) at 3.05) and changes the Met configuration. Another set of mutants prepared by insertion (ins) and/or deletion (Delta) of a valine residue adjacent to Asn64, resulting in modifications in the length of the axial Met-donating loop (NeV65Delta, NeG50N/V65Delta, PaN50G/V65ins), did not result in appreciable alterations of the originally weak (Ne c-552) or very weak (Pa c-551) axial field but had an impact on Met orientation, fluxionality, and relaxation dynamics. Comparison of the electronic fingerprints in the overexpressed proteins and their mutants reveals a linear relationship between axial strain and average paramagnetic heme methyl shifts, irrespective of Met orientation or dynamics. Thus, for these His-Met axially coordinated Fe(III), the large g(max) value EPR signal does not represent a special case as is observed for bis-His axially coordinated Fe(III) with the two His planes perpendicular to each other.

Nitrite controls the release of nitric oxide in Pseudomonas aeruginosa cd1 nitrite reductase

Nitrite reductase (cd1NIR) from Pseudomonas aeruginosa, which catalyses the reduction of nitrite to nitric oxide (NO), contains a c-heme as the electron acceptor and a d1-heme where catalysis occurs. Reduction involves binding of nitrite to the reduced d1-heme, followed by dehydration to yield NO; release of NO and re-reduction of the enzyme close the cycle. Since NO is a powerful inhibitor of ferrous hemeproteins, enzymatic turnover demands the release of NO. We recently discovered that NO dissociation from the ferrous d1-heme is fast, showing that cd1NIR behaves differently from other hemeproteins. Here we demonstrate for the first time that the physiological substrate nitrite displaces NO from the ferrous enzyme, which enters a new catalytic cycle; this reaction depends on the conserved His369 whose role in substrate stabilization is crucial for catalysis. Thus we suggest that also in vivo the activity of cd1NIR is controlled by nitrite.