Insights into Redox Partner Interactions and Substrate Binding in Nitrite Reductase from Alcaligenes xylosoxidans: Crystal Structures of the Trp138His and His313Gln Mutants,

Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator

We report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 Å, showed a striking resemblance with the overall structure of the well-known Class I NirKs composed of two Greek key β-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process.

Recent structural insights into the function of copper nitrite reductases

Copper nitrite reductases (CuNiRs) catalyse the reduction of nitrite to nitric oxide as part of the denitrification pathway. In this review, we describe insights into CuNiR function from structural studies.

Structure and molecular evolution of multicopper blue proteins

The multicopper blue protein family, which contains cupredoxin-like domains as a structural unit, is one of the most diverse groups of proteins. This protein family is divided into two functionally different types of enzymes: multicopper oxidase and nitrite reductase. Multicopper oxidase catalyzes the oxidation of the substrate and then reduces dioxygen. The structures of many multicopper oxidases are already known, and until recently they were classified into two main groups: the three- and six-domain types. Both function as monomers and have three spectroscopically different copper sites: Types I (blue), II, and III (tri-nuclear). Nitrite reductase is a closely related protein that contains Types I and II (mono-nuclear) coppers but reduces nitrite instead of dioxygen. Nitrite reductase, which consists of two domains, forms a homotrimer. Multicopper oxidase and nitrite reductase share similar structural architectures and also contain Type I copper. Therefore, it is proposed that they have a common ancestor protein. Recently, some two-domain type multicopper oxidases have been found and their crystal structures have been determined. They have a trimeric quaternary structure and contain an active site at the molecular interface such as nitrite reductase. These results support previous hypotheses and provide an insight into the molecular evolution of multicopper blue proteins.

Nitrite and nitrite reductases: from molecular mechanisms to significance in human health and disease

Nitrite, previously considered physiologically irrelevant and a simple end product of endogenous nitric oxide (NO) metabolism, is now envisaged as a reservoir of NO to be activated in response to oxygen (O(2)) depletion. In the first part of this review, we summarize and compare the mechanisms of nitrite-dependent production of NO in selected bacteria and in eukaryotes. Bacterial nitrite reductases, which are copper or heme-containing enzymes, play an important role in the adaptation of pathogens to O(2) limitation and enable microrganisms to survive in the human body. In mammals, reduction of nitrite to NO under hypoxic conditions is carried out in tissues and blood by an array of metalloproteins, including heme-containing proteins and molybdenum enzymes. In humans, tissues play a more important role in nitrite reduction, not only because most tissues produce more NO than blood, but also because deoxyhemoglobin efficiently scavenges NO in blood. In the second part of the review, we outline the significance of nitrite in human health and disease and describe the recent advances and pitfalls of nitrite-based therapy, with special attention to its application in cardiovascular disorders, inflammation, and anti-bacterial defence. It can be concluded that nitrite (as well as nitrate-rich diet for long-term applications) may hold promise as therapeutic agent in vascular dysfunction and ischemic injury, as well as an effective compound able to promote angiogenesis.

Linkage isomerization in heme-NOx compounds: understanding NO, nitrite, and hyponitrite interactions with iron porphyrins

Nitric oxide (NO) and its derivatives such as nitrite and hyponitrite are biologically important species of relevance to human health. Much of their physiological relevance stems from their interactions with the iron centers in heme proteins. The chemical reactivities displayed by the heme-NOx species (NOx = NO, nitrite, hyponitrite) are a function of the binding modes of the NOx ligands. Hence, an understanding of the types of binding modes extant in heme-NOx compounds is important if we are to unravel the inherent chemical properties of these NOx metabolites. In this Forum Article, the experimentally characterized linkage isomers of heme-NOx models and proteins are presented and reviewed. Nitrosyl linkage isomers of synthetic iron and ruthenium porphyrins have been generated by photolysis at low temperatures and characterized by spectroscopy and density functional theory calculations. Nitrite linkage isomers in synthetic metalloporphyrin derivatives have been generated from photolysis experiments and in low-temperature matrices. In the case of nitrite adducts of heme proteins, both N and O binding have been determined crystallographically, and the role of the distal H-bonding residue in myoglobin in directing the O-binding mode of nitrite has been explored using mutagenesis. To date, only one synthetic metalloporphyrin complex containing a hyponitrite ligand (displaying an O-binding mode) has been characterized by crystallography. This is contrasted with other hyponitrite binding modes experimentally determined for coordination compounds and computationally for NO reductase enzymes. Although linkage isomerism in heme-NOx derivatives is still in its infancy, opportunities now exist for a detailed exploration of the existence and stabilities of the metastable states in both heme models and heme proteins.

The distal pocket histidine residue in horse heart myoglobin directs the O-binding mode of nitrite to the heme iron

It is now well-established that mammalian heme proteins are reactive with various nitrogen oxide species and that these reactions may play significant roles in mammalian physiology. For example, the ferrous heme protein myoglobin (Mb) has been shown to reduce nitrite (NO(2)(-)) to nitric oxide (NO) under hypoxic conditions. We demonstrate here that the distal pocket histidine residue (His64) of horse heart metMb(III) (i.e., ferric Mb(III)) has marked effects on the mode of nitrite ion coordination to the iron center. X-ray crystal structures were determined for the mutant proteins metMb(III) H64V (2.0 A resolution) and its nitrite ion adduct metMb(III) H64V-nitrite (1.95 A resolution), and metMb(III) H64V/V67R (1.9 A resolution) and its nitrite ion adduct metMb(III) H64V/V67R-nitrite (2.0 A resolution). These are compared to the known structures of wild-type (wt) hh metMb(III) and its nitrite ion adduct hh metMb(III)-nitrite, which binds NO(2)(-) via an O-atom in a trans-FeONO configuration. Unlike wt metMb(III), no axial H(2)O is evident in either of the metMb(III) mutant structures. In the ferric H64V-nitrite structure, replacement of the distal His residue with Val alters the binding mode of nitrite from the nitrito (O-binding) form in the wild-type protein to a weakly bound nitro (N-binding) form. Reintroducing a H-bonding residue in the H64V/V67R double mutant restores the O-binding mode of nitrite. We have also examined the effects of these mutations on reactivities of the metMb(III)s with cysteine as a reducing agent and of the (ferrous) Mb(II)s with nitrite ion under anaerobic conditions. The Mb(II)s were generated by reduction of the Mb(III) precursors in a second-order reaction with cysteine, the rate constants for this step following the order H64V/V67R > H64V >> wt. The rate constants for the oxidation of the Mb(II)s by nitrite (giving NO as the other product) follow the order wt > H64V/V67R >> H64V and suggest a significant role of the distal pocket H-bonding residue in nitrite reduction.

The structure of the Met144Leu mutant of copper nitrite reductase from Alcaligenes xylosoxidans provides the first glimpse of a protein–protein complex with azurin II

Cu-containing nitrite reductases (NiRs) perform the reduction of nitrite to NO via an ordered mechanism in which the delivery of a proton and an electron to the catalytic type 2 Cu site is highly orchestrated. Electron transfer from a redox partner protein, azurin or pseudoazurin, to the type 1 Cu site is assumed to occur through the formation of a protein-protein complex. We report here a new crystal form in space group P2(1)2(1)2(1) of the Met144Leu mutant of NiR from Alcaligenes xylosoxidans (AxNiR), revealing a head-to-head packing motif involving residues around the hydrophobic patch of domain 1. Superposition of the structure of azurin II with that of domain 1 of one of the Met144Leu molecules provides the first glimpse of an azurin II-NiR protein-protein complex. Mutations of two of the residues of AxNiR, Trp138His (Barrett et al. in Biochemistry 43:16311-16319, 2004) and Met87Leu, highlighted in the AxNiR-azurin complex, results in substantially decreased activity when azurin is used as the electron donor instead of methyl viologen, providing direct evidence for the importance of this region for complex formation.

Mechanism of Nitrite Reduction at T2Cu Centers: Electronic Structure Calculations of Catalysis by Copper Nitrite Reductase and by Synthetic Model Compounds

The mechanism of nitrite reduction at the Cu(II) center of both copper nitrite reductase and a number of corresponding synthetic models has been investigated by using both QM/MM and cluster calculations employing density functional theory methods. The mechanism in both cases is found to be very similar. Initially nitrite is bound in a bidentate fashion to the Cu(II) center via the two oxygen atoms. Upon reduction of the copper center, the two possible coordination modes of the protonated nitrite, by either nitrogen or a single oxygen atom, are close in energy, with nitrogen coordination probably preferred. Further protonation of this species leads to N-O bond cleavage, and an electron transfer from the Cu(I) center to the N-O+ ligand, resulting in loss of NO and regeneration of the resting state of the enzyme having a bound water molecule.

pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.

Crystal structures of the nitrite and nitric oxide complexes of horse heart myoglobin

Nitrite is an important species in the global nitrogen cycle, and the nitrite reductase enzymes convert nitrite to nitric oxide (NO). Recently, it has been shown that hemoglobin and myoglobin catalyze the reduction of nitrite to NO under hypoxic conditions. We have determined the 1.20 A resolution crystal structure of the nitrite adduct of ferric horse heart myoglobin (hh Mb). The ligand is bound to iron in the nitrito form, and the complex is formulated as MbIII(ONO-). The Fe-ONO bond length is 1.94 A, and the O-N-O angle is 113 degrees . In addition, the nitrite ligand is stabilized by hydrogen bonding with the distal His64 residue. We have also determined the 1.30 A resolution crystal structures of hh MbIINO. When hh MbIINO is prepared from the reaction of metMbIII with nitrite/dithionite, the FeNO angle is 144 degrees with a Fe-NO bond length of 1.87 A. However, when prepared from the reaction of NO with reduced MbII, the FeNO angle is 120 degrees with a Fe-NO bond length of 2.13 A. This difference in FeNO conformations as a function of preparative method is reproducible, and suggests a role of the distal pocket in hh MbIINO in stabilizing local FeNO conformational minima.

Structural insights into enzyme-substrate interaction and characterization of enzymatic intermediates of organic hydroperoxide resistance protein from Xylella fastidiosa

Organic hydroperoxide resistance proteins (Ohr) belong to a family of proteins that possess thiol-dependent peroxidase activity endowed by reactive cysteine residues able to reduce peroxides. The crystal structure of Ohr from Xylella fastidiosa in complex with polyethylene glycol, providing insights into enzyme-substrate interactions is described herein. In addition, crystallographic studies, molecular modeling and biochemical assays also indicated that peroxides derived from long chain fatty acids could be the biological substrates of Ohr. Because different oxidation states of the reactive cysteine were present in the Ohr structures from X. fastidiosa, Pseudomonas aeruginosa and Deinococcus radiodurans it was possible to envisage a set of snapshots along the coordinate of the enzyme-catalyzed reaction. The redox intermediates of X. fastidiosa Ohr observed in the crystals were further characterized in solution by electrospray ionization mass spectrometry and by biochemical approaches. In this study, the formation of an intramolecular disulfide bond and oxidative inactivation through the formation of a sulfonic acid derivative was unequivocally demonstrated for the first time. Because Ohr proteins are exclusively present in bacteria, they may represent promising targets for therapeutical drugs. In this regard, the structural and functional analyses of Ohr presented here might be very useful.

Roles of Trp144 and Tyr203 in copper-containing nitrite reductase from Achromobacter cycloclastes IAM1013

The roles of the Trp144 and Tyr203 residues near the type 1 Cu site of Achromobacter cycloclastes nitrite reductase (AcNIR) have been examined with mutants of AcNIR. Tyr203 is located on the protein surface near the type 1 Cu site of AcNIR, and Trp144 is between the Tyr203 and the type 1 Cu center in AcNIR. Single mutation of Trp144 or Tyr203 in AcNIR to Leu resulted in decreased rate constants of intermolecular electron transfer from its cognate pseudoazurin (AcPAZ) (k(ET)=1.9x10(5), 2.2x10(5), and 7.3x10(5)M(-1)s(-1) for W144L, Y203L, and wild-type AcNIR, respectively). The intermolecular electron transfer rate constant of double mutant AcNIR (W144L/Y203L) was the same as those of single mutants (k(ET)=1.9x10(5)M(-1)s(-1) for W144L/Y203L). The redox potentials, coordination structures of the type 1 Cu, and the enzyme activities of AcNIR were affected little by the mutation.

Pseudoazurin-Nitrite Reductase Interactions

The nitrite reductase-binding site on pseudoazurin has been determined by using NMR chemical-shift perturbations. It comprises residues in the hydrophobic patch surrounding the exposed copper ligand His81 as well as several positively charged residues. The binding site is similar for both redox states of pseudoazurin, despite differences in the binding mode. The results suggest that pseudoazurin binds in a well-defined orientation. Docking simulations provide a putative structure of the complex with a binding site on nitrite reductase that has several hydrophobic and polar residues as well as a ridge of negatively charged side chains and a copper-to-copper distance of 14 A.

Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism

Copper-containing nitrite reductases catalyze the reduction of nitrite to nitric oxide (NO), a key step in denitrification that results in the loss of terrestrial nitrogen to the atmosphere. They are found in a wide variety of denitrifying bacteria and fungi of different physiology from a range of soil and aquatic ecosystems. Structural analysis of potential intermediates in the catalytic cycle is an important goal in understanding enzyme mechanism. Using "crystal harvesting" and substrate-soaking techniques, we have determined atomic resolution structures of four forms of the green Cu-nitrite reductase, from the soil bacterium Achromobacter cycloclastes. These structures are the resting state of the enzyme at 0.9 A, two species exhibiting different conformations of nitrite bound at the catalytic type 2 Cu, one of which is stable and also has NO present, at 1.10 A and 1.15 A, and a stable form with the product NO bound side-on to the catalytic type 2 Cu, at 1.12 A resolution. These structures provide incisive insights into the initial binding of substrate, its repositioning before catalysis, bond breakage (O-NO), and the formation of a stable NO adduct.