Manganese superoxide dismutase from Thermus thermophilus. A structural model refined at 1.8 A resolution

Spectroscopic and computational insights into second-sphere amino-acid tuning of substrate analogue/active-site interactions in iron(III) superoxide dismutase

In this study, the mechanism by which second-sphere residues modulate the structural and electronic properties of substrate-analogue complexes of the Fe-dependent superoxide dismutase (FeSOD) has been explored. Both spectroscopic and computational methods were used to investigate the azide (N3(-)) adducts of Fe(3+)SOD (N3-Fe(3+)SOD) and its Q69E mutant, as well as Fe(3+)-substituted MnSOD (N3-Fe(3+)(Mn)SOD) and its Y34F mutant. Electronic absorption, circular dichroism, and magnetic circular dichroism spectroscopic data reveal that the energy of the dominant N3(-)-->Fe(3+) ligand-to-metal charge transfer (LMCT) transition decreases in the order N3-Fe(3+)(Mn)SOD>N3-Fe(3+)SOD>Q69E N3-Fe(3+)SOD. Intriguingly, the LMCT transition energies correlate almost linearly with the Fe(3+/2+) reduction potentials of the corresponding Fe(3+)-bound SOD species in the absence of azide, which span a range of approximately 1 V (see the preceding paper). To explore the origin of this correlation, combined quantum mechanics/molecular mechanics (QM/MM) geometry optimizations were performed on complete enzyme models. The INDO/S-CI computed electronic transition energies satisfactorily reproduce the experimental trend in LMCT transition energies, indicating that the QM/MM optimized active-site models are reasonable. Density functional theory calculations on these experimentally validated active-site models reveal that the differences in spectral and electronic properties among the four N 3(-) adducts arise primarily from differences in the hydrogen-bond network involving the conserved second-sphere Gln (mutated to Glu in Q69E FeSOD) and the solvent ligand. The implications of our findings with respect to the mechanism by which the second-coordination sphere modulates substrate-analogue binding as well as the catalytic properties of FeSOD are discussed.

Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring

A new gene encoding a thermostable Fe-superoxide dismutase (tcSOD) was identified from a metagenomic library prepared from a hot spring sample. The open reading frame of tcSOD encoded a 211 amino acid protein. The recombinant protein was overexpressed in Escherichia coli and confirmed to be a Fe-SOD with a specific activity of 1,890 U/mg using the pyrogallol method. The enzyme was highly stable at 80 degrees C and retained 50% activity after heat treatment at 95 degrees C for 2 h. It showed striking stability across a wide pH span from 4 to 11. The native form of the enzyme was determined as a homotetramer by analytical ultracentrifugation and gradient native polyacrylamide gel electrophoresis. Fe(2+) was found to be important to SOD activity and to the stability of tcSOD dimer. Comparative modeling analyses of tcSOD tetramer indicate that its high thermostability is mainly due to the presence of a large number of intersubunit ion pairs and hydrogen bonds and to a decrease in solvent accessible hydrophobic surfaces.

Manganese binding to the 23 kDa extrinsic protein of Photosystem II

The recombinant form of the extrinsic 23 kDa protein (psbP) of Photosystem II (PSII) was studied with respect to its capability to bind Mn. The stoichiometry was determined to be one manganese bound per protein. A very high binding constant, K(A)=10(-17) M(-1), was determined by dialysis of the Mn containing protein against increasing EDTA concentration. High Field EPR spectroscopy was used to distinguish between specific symmetrically ligated Mn(II) from those non-specifically Mn(II) attached to the protein surface. Upon Mn binding PsbP exhibited fluorescence emission with maxima at 415 and 435 nm when tryptophan residues were excited. The yield of this blue fluorescence was variable from sample to sample. It was likely that different conformational states of the protein were responsible for this variability. The importance of Mn binding to PsbP in the context of photoactivation of PSII is discussed.

Leishmania aethiopica: Strain identification and characterization of superoxide dismutase-B genes

This study was performed to characterize the genes that code for superoxide dismutase (SOD) in Leishmania aethiopica. It involved three main steps: specimen collection and parasite isolation, species identification, and molecular characterization of the SOD genes. Out of 20 skin slit specimens cultured and processed from suspected cutaneous leishmaniasis patients enrolled in the study, five (25%) were found to be positive for motile promastigotes. Isoenzyme electrophoresis and PCR-RFLP results confirmed that the isolates were L. aethiopica. Superoxide dismutase-B (SODB) genes were identified from L. aethiopica for the first time. Iron superoxide dismutase-B genes amplified from promastigotes of L. aethiopica (LaeFeSODB) were similar in size to the SODB genes of other Leishmania species. Nucleotide sequences of LaeFeSODB1 showed 95.4, 93.5, and 97.3% identity with L. donovani SODB1 (LdFeSODB1) L. major SODB1 (LmFeSODB1) and L. tropica SODB1 (LtrFeSODB1), respectively. Similarly, LaeFeSODB2 showed 95.9 and 94.1 and 97.6% identity with LdFeSODB2 and LmFeSODB2 and LtrFeSODB2, respectively. On the other hand, predicted amino acid sequence comparison indicated that LaeFeSODB1 had 91.3, 89.8, and 93.9% identity with LdFeSODB1, LmFeSODB1, and LtrFeSODB1, respectively. The difference in nucleic acid sequence of LaeFeSODB from that of LmFeSODB and LtrFeSODB can be utilized to develop specific molecular methods that help differentiate these species in places where there is an overlap in the distribution of these species. In addition, the data provide information about the situation of L. aethiopica with respect to SODB genes.

Effects of Substrate Analogues and pH on Manganese Superoxide Dismutases

The effect of the substrate analogues azide and fluoride on the manganese(II) zero-field interactions of different manganese-containing superoxide dismutases (SOD) was measured using high-field electron paramagnetic resonance spectroscopy. Two cambialistic types, proteins that are active with manganese or iron, were studied along with two that were only active with iron and another that was only active with manganese. It was found that azide was able to coordinate directly to the pentacoordinated Mn(II) site of only the MnSOD from Escherichia coli and the cambialistic SOD from Rhodobacter capsulatus. The formation of a hexacoordinate azide-bound center was characterized by a large reduction in the Mn(II) zero-field interaction. In contrast, all five SODs were affected by fluoride, but no evidence for hexacoordinate Mn(II) formation was detected. For both azide and fluoride, the extent of binding was no more than 50%, implying either that a second binding site was present or that binding was self-limiting. Only the Mn(II) zero-field interactions of the two SODs that had little or no activity with manganese were found to be significantly affected by pH, the manganese-substituted iron superoxide dismutase from E. coli and the Gly155Thr mutant of the cambialistic SOD from Porphyromonas gingivalis. A model for anion binding and the observed pK involving tyrosine-34 is presented.

Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance

Background

Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria.

Results

By reconstructing the evolution of Thermus and Deinococcus after the divergence from their common ancestor, we demonstrate a high level of post-divergence gene flux in both lineages. Various aspects of the adaptation to high temperature in Thermus can be attributed to horizontal gene transfer from archaea and thermophilic bacteria; many of the horizontally transferred genes are located on the single megaplasmid of Thermus. In addition, the Thermus lineage has lost a set of genes that are still present in Deinococcus and many other mesophilic bacteria but are not common among thermophiles. By contrast, Deinococcus seems to have acquired numerous genes related to stress response systems from various bacteria. A comparison of the distribution of orthologous genes among the four partitions of the Deinococcus genome and the two partitions of the Thermus genome reveals homology between the Thermus megaplasmid (pTT27) and Deinococcus megaplasmid (DR177).

Conclusion

After the radiation from their common ancestor, the Thermus and Deinococcus lineages have taken divergent paths toward their distinct lifestyles. In addition to extensive gene loss, Thermus seems to have acquired numerous genes from thermophiles, which likely was the decisive contribution to its thermophilic adaptation. By contrast, Deinococcus lost few genes but seems to have acquired many bacterial genes that apparently enhanced its ability to survive different kinds of environmental stresses. Notwithstanding the accumulation of horizontally transferred genes, we also show that the single megaplasmid of Thermus and the DR177 megaplasmid of Deinococcus are homologous and probably were inherited from the common ancestor of these bacteria.

Probing the Geometric and Electronic Structures of the Low-Temperature Azide Adduct and the Product-Inhibited Form of Oxidized Manganese Superoxide Dismutase

The geometric and electronic structures of the six-coordinate azide adduct of oxidized manganese superoxide dismutase (Mn3+ SOD) that is formed at low temperatures, LT N3-Mn3+ SOD, has been examined in detail through a combined spectroscopic/computational approach. Electronic absorption, circular dichroism (CD), magnetic CD (MCD) and variable-temperature, variable-field (VTVH) MCD spectroscopies were used to determine electronic transition energies and to obtain an estimate of zero-field splitting parameters for LT N3-Mn3+ SOD. These experimental data were utilized in conjunction with semiempirical intermediate neglect of differential overlap/spectroscopic parametrization-configuration interaction (INDO/S-CI) and time-dependent density functional theory (TD-DFT) computations to evaluate hypothetical active-site models of LT N3-Mn3+ SOD generated by constrained DFT geometry optimizations. Collectively, our spectroscopic/computational results indicate that N3- binding to Mn3+ SOD at low temperatures promotes neither protonation of the axial solvent ligand nor reorientation of the redox-active molecular orbital, both of which had been previously suggested. Using the same experimentally validated computational approach, models of the product-inhibited form of MnSOD were also developed and evaluated by their relative energies and TD-DFT-computed absorption spectra. On the basis of our computational results as well as previously published kinetic data, we propose that the product-inhibited form of MnSOD is best described as a side-on peroxo-Mn3+ adduct possessing an axial H2O ligand. Notably, attempts to generate a stable hydroperoxo-Mn3+ SOD species by protonation of the proximal O atom of the hydroperoxo ligand resulted in dissociation of HOO- and eventual H+ transfer from Tyr34 to HOO-, generating deprotonated Tyr34 and H2O2. The implications of these results with respect to the mechanism of O2*- dismutation by MnSOD are discussed.

Spectroscopic and computational studies of the azide-adduct of manganese superoxide dismutase: definitive assignment of the ligand responsible for the low-temperature thermochromism

A variety of spectroscopic and computational techniques have been used to examine the thermochromic transition previously reported for the oxidized state of Mn-dependent superoxide dismutase from E. coli in the presence of substrate analog azide (N(3)-Mn(3+)SOD).[Whittaker, M. M.; Whittaker, J. W. Biochemistry 1996, 35, 6762-6770.] Although previous spectroscopic studies had shown that this thermochromic event corresponds to a change in coordination number of the active-site Mn(3+) ion from 6 to 5 as temperature is increased, the ligand that dissociates in this conversion had yet to be identified. Through the use of electronic absorption, circular dichroism (CD), and magnetic CD (MCD) spectroscopies, both d-->d and ligand-to-metal charge-transfer (LMCT) transition energies have been determined for native Mn(3+)SOD (possessing a five-coordinate Mn(3+) center) and Y34F N(3)-Mn(3+)SOD (forming a six-coordinate N(3)-Mn(3+) adduct at all temperatures). These two systems provide well-defined reference points from which to analyze the absorption and CD data obtained for N(3)-Mn(3+)SOD at room temperature (RT). Comparison of excited-state spectroscopic data reveals that Mn(3+)SOD and RT N(3)-Mn(3+)SOD exhibit virtually identical d-->d transition energies, suggesting that these two species possess similar geometric and electronic structures and, thus, that azide does not actually coordinate to the active-site Mn(3+) ion at RT. However, resonance Raman spectra of both N(3)-Mn(3+)SOD and Y34F N(3)-Mn(3+)SOD at 0 degrees C exhibit azide-related vibrations, indicating that azide does interact with the active site of the native enzyme at this temperature. To gain further insight into the nature of the azide/Mn(3+) interaction in RT N(3)-Mn(3+)SOD, several viable active-site models designed to promote either dissociation of coordinated solvent, Asp167, or azide were generated using DFT computations. By utilizing the time-dependent DFT method to predict absorption spectra for these models of RT N(3)-Mn(3+)SOD, we demonstrate that only azide dissociation is consistent with experimental data. Collectively, our spectroscopic and computational data provide evidence that the active site of N(3)-Mn(3+)SOD at RT exists in a dynamic equilibrium, with the azide molecule either hydrogen-bonded to the second-sphere Tyr34 residue or coordinated to the Mn(3+) ion. These results further highlight the role that second-sphere residues, especially Tyr34, play in tuning substrate (analog)/metal ion interactions.

A molecular modeling and QSAR study of suppressors of the growth of Trypanosoma cruzi epimastigotes

In this work, we have used molecular modeling and QSAR tools to study 18 dithiocarbamate suppressors of the growth of Trypanosoma cruzi epimastigotes, which have been reported in the literature as superoxide dismutase (SOD) inhibitors. The principal component analysis (PCA) showed that the descriptors superficial area, heat of formation, logarithm of the partition coefficient, charge of the nitrogen atom from the dithiocarbamate group and Charges of the two carbon atoms adjacent to that nitrogen are responsible for the classification between the higher and lower trypanomicid activity. Using multiple linear regression (MLR) and docking methods it was possible to identify the probable bioactive isomers that suppress of the growth of T. cruzi epimastigotes. Our best partial least square (PLS) model obtained with these six descriptors yields a good correlation between experimental and predicted biological activities and compares two different SODs as possible target for interaction with the dithiocarbamates.

Electrochemistry and Electrocatalytic Activities of Superoxide Dismutases at Gold Electrodes Modified with a Self-Assembled Monolayer

In this article, the electrochemical properties and electrocatalytic activity of three kinds of superoxide dismutases (SODs), that is, bovine erythrocyte copper-zinc superoxide dismutase (Cu/Zn-SOD), iron superoxide dismutase from Escherichia coli (Fe-SOD), and manganese superoxide dismutase from E. coli (Mn-SOD), in the SOD family were studied. It was revealed that the direct electron transfer of the three kinds of SODs could be efficiently promoted by a self-assembled monolayer (SAM) of 3-mercaptopropionic acid (MPA) confined on a gold electrode. The electrochemical properties of the SODs at the MPA-SAM electrode vary with the sort of SOD with respect to the formal potential, reversibility of electrode reactions, kinetic parameters, and pH dependence, suggesting different mechanisms for the electrode reactions of the individual SODs. A combination of the facilitated direct electron transfer and the bifunctional enzymatic catalytic activities of the SODs via a redox cycle of their active metals substantially offered a flexible electrochemical route to determination of O(2)(*)(-) where O(2)(*)(-) can be sensed with the SOD-based biosensors in both anodic and cathodic polarizations. Such an intrinsic feature of the SOD-based biosensors successfully enabled a sensitive determination scheme for O(2)(*)(-) free from the interference from some coexisting electroactive species, such as ascorbic acid (AA) and uric acid (UA). Further potential applications for in vivo determination of O(2)(*)(-) is also suggested.

Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases

The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+ and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four betaalphabetabetabeta modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.

Specificity and Phenetic Relationships of Iron- and Manganese-containing Superoxide Dismutases on the Basis of Structure and Sequence Comparisons

The iron- and manganese-containing superoxide dismutases (Fe/Mn-SOD) share the same chemical function and spatial structure but can be distinguished according to their modes of oligomerization and their metal ion specificity. They appear as homodimers or homotetramers and usually require a specific metal for activity. On the basis of 261 aligned SOD sequences and 12 superimposed x-ray structures, two phenetic trees were constructed, one sequence-based and the other structure-based. Their comparison reveals the imperfect correlation of sequence and structural changes; hyperthermophilicity requires the largest sequence alterations, whereas dimer/tetramer and manganese/iron specificities are induced by the most sizable structural differences within the monomers. A systematic investigation of sequence and structure characteristics conserved in all aligned SOD sequences or in subsets sharing common oligomeric and/or metal specificities was performed. Several residues were identified as guaranteeing the common function and dimeric conformation, others as determining the tetramer formation, and yet others as potentially responsible for metal specificity. Some form cation-pi interactions between an aromatic ring and a fully or partially positively charged group, suggesting that these interactions play a significant role in the structure and function of SOD enzymes. Dimer/tetramer- and iron/manganese-specific fingerprints were derived from the set of conserved residues; they can be used to propose selected residue substitutions in view of the experimental validation of our in silico derived hypotheses.

A high-frequency and high-field EPR study of new azide and fluoride mononuclear Mn(III) complexes

The isolation, structural characterization and electronic properties of three new six-coordinated Mn(III) complexes, [Mn(bpea)(F)(3)] (1), [Mn(bpea)(N(3))(3)] (2), and [Mn(terpy)(F)(3)] (3) are reported (bpea = N,N-bis(2-pyridylmethyl)-ethylamine; terpy = 2,2':6',2' '-terpyridine). As for [Mn(terpy)(N(3))(3)] (4) (previously described by Limburg J.; Vrettos J. S.; Crabtree R. H.; Brudvig G. W.; de Paula J. C.; Hassan A.; Barra A-L.; Duboc-Toia C.; Collomb M-N. Inorg. Chem. 2001, 40, 1698), all these complexes exhibit a Jahn-Teller distortion of the octahedron characteristic of high-spin Mn(III) (S = 2). The analysis of the crystallographic data shows an elongation along the tetragonal axis of the octahedron for complexes 1 and 3, while complex 2 presents an unexpected compression. The electronic properties were investigated using a high-field and high-frequency EPR study performed between 5 and 15 K (190-575 GHz). The spin Hamiltonian parameters determined in solid state are in agreement with the geometry of the complexes observed in the crystal structures. A negative D value found for 1 and 3 is related to the elongated tetragonal distortion, whereas the positive D value determined for 2 is in accordance with a compressed octahedron. The high E/D values, in the range of 0.103 to 0.230 for all complexes, are correlated with the highly distorted geometry present around the Mn(III) ion. HF-EPR experiments were also performed on complex 1 in solution and show that the D value is the only spin Hamiltonian parameter which is slightly modified compared to the solid state (D = -3.67 cm(-1) in solid state; D = -3.95 cm(-1) in solution).

Pronounced conversion of the metal-specific activity of superoxide dismutase from Porphyromonas gingivalis by the mutation of a single amino acid (Gly155Thr) located apart from the active site

Glycine 155, which is located approximately 10 A from the active metal sites, is mostly conserved in aligned amino acid sequences of manganese-specific superoxide dismutases (Mn-SODs) and cambialistic SOD (showing the same activity with Fe and Mn) from Porphyromonas gingivalis, but is substituted for threonine in most Fe-SODs. Since Thr155 is located between Trp123 and Trp125, and Trp123 is one member of the metal-surrounding aromatic amino acids, there is a possibility that the conversion of this amino acid may cause a conversion of the metal-specific activity of cambialistic P. gingivalis SOD. To clarify this possibility, we have prepared a mutant of the P. gingivalis SOD with conversion of Gly155 to Thr. The ratios of the specific activities of Fe- to Mn-reconstituted enzyme, which are measured by the xanthine oxidase/cytochrome c method, increased from 0.6 in the wild-type to 11.2 in the mutant SODs, indicating the conversion of the metal-specific activity of the enzyme from a cambialistic type to an Fe-specific type. The visible absorption spectra of the Fe- and Mn-reconstituted mutant SODs closely resembled those of Fe-specific SOD. Furthermore, the EPR spectra of the Fe- and Mn-reconstituted mutant SODs also closely resembled those of Fe-specific SOD. Three-dimensional structures of the Fe-reconstituted wild-type SOD and Mn-reconstituted mutant SOD have been determined at 1.6 A resolution. Both structures have identical conformations, orientations of residues involved in metal binding, and hydrogen bond networks, while the side chain of Trp123 is moved further toward the metal-binding site than in wild-type SOD. A possible contribution of the structural differences to the conversion of the metal-specific activity through rearrangement of the hydrogen bond network among Trp123, Gln70, Tyr35, and the metal-coordinated solvent is discussed.

Spectroscopic and computational study of a non-heme iron [Fe-NO]7 system: exploring the geometric and electronic structures of the nitrosyl adduct of iron superoxide dismutase

Like many non-heme iron enzymes, reduced iron superoxide dismutase (Fe(2+)SOD) reacts with nitric oxide (NO) to yield an [Fe-NO]7 system. Electron paramagnetic resonance (EPR) data obtained for this Fe-NO adduct of FeSOD (NO-FeSOD) exhibit two rhombic S = 3/2 signals of comparable population; E/D = 0.128 (42%) and 0.154 (58%). While similar results were previously reported for NO-FeSOD [Niederhoffer, E. C.; Fee, J. A.; Papaefthymiou, V.; Münck, E. Magnetic Resonance Studies Involving Iron Superoxide Dismutase from Escherichia coli. Isotope and Nuclear Chemistry Division Annual Report; Los Alamos National Laboratory: Los Alamos, NM, 1987], detailed geometric and electronic structure descriptions of these [Fe-NO]7 systems had not yet been developed. Therefore, in addition to EPR spectroscopy, we have used electronic absorption, magnetic circular dichroism (MCD), variable-temperature, variable-field MCD, and resonance Raman spectroscopies to determine ground-state spin Hamiltonian parameters, electronic transition energies, oscillator strengths, and transition polarizations for NO-FeSOD. These spectroscopic parameters have been used in conjunction with density functional theory (DFT) and semiempirical INDO/S-CI calculations to generate an experimentally calibrated active site model for NO-FeSOD. Our studies indicate that NO binds to the active site of Fe(2+)SOD to form a six-coordinate [Fe-NO]7 system with an Fe-N-O angle of approximately 145 degrees. DFT computations performed on this model of NO-FeSOD reveal that the NO ligand is formally reduced by the ferrous center to yield NO(-) and an Fe(3+) center that are strongly antiferromagnetically coupled. DFT calculations reveal that NO binding to Fe(2+)SOD also lowers the pK of the coordinated water ligand by at least 3.3 pH units, suggesting that this process is associated with increased acidity and probable ionization of the axial solvent ligand. To explore the origin of the two [Fe-NO]7 systems observed by EPR spectroscopy, additional calculations have been performed on slightly perturbed NO-FeSOD models. Significantly, semiempirical INDO/S-CI computations reveal that the rhombicity of NO-FeSOD is altered by changes in the Fe-N-O angle or rotation about the Fe-N(O) bond, suggesting that the two species observed by EPR spectroscopy merely differ slightly with respect to the orientation of the NO ligand. Indeed, our EPR data obtained on NO-FeSOD variants indicate that the relative population of the S = 3/2 signals can be altered by perturbations in the second sphere of the protein active site. These results provide compelling evidence that the second coordination sphere is able to modulate the geometric and electronic structures of NO-FeSOD.

Comparison and contrasts between the active site PKs of Mn-superoxide dismutase and those of Fe-superoxide dismutase

The Fe- and Mn-containing superoxide dismutases catalize the same reaction and have almost superimposable active sites. Therefore, the details of their mechanisms have been assumed to be similar. However, we now show that the pH dependence of Escherichia coli MnSOD activity reflects a different active site proton equilibrium in (oxidized) Mn(3+)SOD than the event that affects the active site pK of oxidized FeSOD. We find that the universally conserved Tyr34 that has a pK above 11.5 in Fe(3+)SOD is responsible for the pK near 9.5 of Mn(3+)SOD and, thus, that the oxidized state pK of Mn(3+)SOD corresponds to an outer-sphere event whereas that of Fe(3+)SOD corresponds to an inner sphere event [Bull, C.; Fee, J. A. J. Am. Chem. Soc. 1985, 107, 3295-3304]. We also present the first description of a reduced-state pK for MnSOD. Mn(2+)SOD's pK involves deprotonation of Tyr34, as does Fe(2+)SOD's pK [Sorkin, D. L.; Miller A.-F. Biochemistry 1997, 36, 4916-4924]. However, the values of the pKs, 10.5 and 8.5 respectively, are quite different and Mn(2+)SOD's pK affects the coordination geometry of Mn(2+), most likely via polarization of the conserved Gln146 that hydrogen bonds to axially coordinated H(2)O. Our findings are consistent with the different electronic configurations of Mn(2+/3+) vs Fe(2+/3+), such as the stronger hydrogen bonding between Gln146 and coordinated solvent in MnSOD than that between the analogous Gln69 and coordinated solvent in FeSOD, and the existence of weakly localized H(2)O near the sixth coordination site of Mn(2+) in Mn(2+)SOD [Borgstahl et al. J. Mol. Biol. 2000, 296, 951-959].

Biochemical characterization of a membrane-bound manganese-containing superoxide dismutase from the cyanobacterium Anabaena PCC 7120

The filamentous cyanobacterium Anabaena PCC 7120 (now renamed Nostoc PCC 7120) possesses two genes for superoxide dismutase (SOD). One is an iron-containing (FeSOD) whereas the other is a manganese-containing superoxide dismutase (MnSOD). Localization experiments and analysis of the sequence showed that the FeSOD is cytosolic, whereas the MnSOD is a membrane-bound homodimeric protein containing one transmembrane helix, a spacer region, and a soluble catalytic domain. It is localized in both cytoplasmic and thylakoid membranes at the same extent with the catalytic domains positioned either in the periplasm or the thylakoid lumen. A phylogenetic analysis revealed that generally the highly homologous MnSODs of filamentous cyanobacteria are unique in being membrane-bound. Two recombinant variants of Anabaena MnSOD lacking either the hydrophobic region (MnSOD(Delta 28)) or the hydrophobic and the linker region (MnSOD(Delta 60)) are shown to exhibit the characteristic manganese peak at 480 nm, an almost 100% occupancy of manganese per subunit, a specific activity using the ferricytochrome assay of (660 +/- 90) unit mg-1 protein and a dissociation constant for the inhibitor azide of (0.84 +/- 0.05) mm. Using stopped-flow spectroscopy it is shown that the decay of superoxide in the presence of various (MnSOD(Delta 28)) or (MnSOD(Delta 60)) concentrations is first-order in enzyme concentration allowing the calculation of catalytic rate constants which increase with decreasing pH: 8 x 10(6) m-1 s-1 (pH 10) and 6 x 10(7) m-1 s-1 (pH 7). The physiological relevance of these findings is discussed with respect to the bioenergetic peculiarities of cyanobacteria.

Thermostability of manganese- and iron-superoxide dismutases from Escherichia coli is determined by the characteristic position of a glutamine residue

The structurally homologous mononuclear iron and manganese superoxide dismutases (FeSOD and MnSOD, respectively) contain a highly conserved glutamine residue in the active site which projects toward the active-site metal centre and participates in an extensive hydrogen bonding network. The position of this residue is different for each SOD isoenzyme (Q69 in FeSOD and Q146 in MnSOD of Escherichia coli). Although site-directed mutant enzymes lacking this glutamine residue (FeSOD[Q69G] and MnSOD[Q146A]) demonstrated a higher degree of selectivity for their respective metal, they showed little or no activity compared with wild types. FeSOD double mutants (FeSOD[Q69G/A141Q]), which mimic the glutamine position in MnSOD, elicited 25% the activity of wild-type FeSOD while the activity of the corresponding MnSOD double mutant (MnSOD[G77Q/Q146A]) increased to 150% (relative to wild-type MnSOD). Both double mutants showed reduced selectivity toward their metal. Differences exhibited in the thermostability of SOD activity was most obvious in the mutants that contained two glutamine residues (FeSOD[A141Q] and MnSOD[G77Q]), where the MnSOD mutant was thermostable and the FeSOD mutant was thermolabile. Significantly, the MnSOD double mutant exhibited a thermal-inactivation profile similar to that of wild-type FeSOD while that of the FeSOD double mutant was similar to wild-type MnSOD. We conclude therefore that the position of this glutamine residue contributes to metal selectivity and is responsible for some of the different physicochemical properties of these SODs, and in particular their characteristic thermostability.

Spectroscopic and computational studies on iron and manganese superoxide dismutases: nature of the chemical events associated with active-site pKs

A combined spectroscopic/computational approach has been utilized to explore the chemical origins of the active-site pKs of the structurally homologous Fe- and Mn-dependent superoxide dismutases (SODs). Absorption, circular dichroism, magnetic circular dichroism, and variable-temperature, variable-field magnetic circular dichroism spectroscopic experiments have permitted us to determine electronic transition energies and polarizations, as well as ground-state spin Hamiltonian parameters. These experimental data have been used in conjunction with semiempirical intermediate neglect of differential overlap/spectroscopic parametrization configuration interaction (INDO/S-CI) computations for evaluating hypothetical active-site models for the high-pH species generated by density functional theory (DFT) geometry optimizations. Our experimental and computational data indicate that both reduced FeSOD and oxidized MnSOD do not bind hydroxide at high pH; rather, the active-site pK for these two species is attributed to deprotonation of a second-sphere tyrosine. Conversely, our data obtained on oxidized FeSOD indicate that hydroxide binding is responsible for the observed active-site pK for this species. Intriguingly, in the Fe-substituted form of MnSOD this identical chemical event occurs at a significantly lower pH. Overall, our results suggest an important role for second-sphere amino acids in tuning the active sites' interaction with small anions and bring into question the assumption that these homologous enzymes operate by the same molecular mechanism.

Three-dimensional structure of manganese superoxide dismutase from Bacillus halodenitrificans, a component of the so-called "green protein"

A so-called "green protein" has been purified from a moderate halophilic eubacterium, Bacillus halodenitrificans (ATCC 49067), under anaerobic conditions. The protein, which might play an important role in denitrification, dissociates mainly into two components after exposure to air: a manganese superoxide dismutase (GP-MnSOD) and a nucleoside diphosphate kinase. As a first step in elucidating the overall structure of the green protein and the role of each component, the 2.8-A resolution crystal structure of GP-MnSOD was determined. Compared with other manganese dismutases, GP-MnSOD shows two significant characteristics. The first is that the entrance to its substrate channel has an additional basic residue-Lys38. The second is that its surface is decorated with an excess of acidic over basic residues. All these structural features may be related to GP-MnSOD's high catalytic activity and its endurance against the special cytoplasm of B. halodenitrificans. The structure of GP-MnSOD provides the basis for recognizing its possible role and assembly state in the green protein.

The 2.0A resolution structure of the catalytic portion of a cyanobacterial membrane-bound manganese superoxide dismutase

Cyanobacteria are shown to be unique in containing membrane-bound manganese superoxide dismutases (MnSOD). They are homodimeric type 2 membrane proteins that protect this phototrophic organism against oxidative stress. We have determined, for the first time, the 2.0A resolution structure of the catalytic portion of the MnSOD from the filamentous cyanobacterium Anabaena PCC 7120. Within each subunit, both the N-terminal helical hairpin (His94 and His145) and the C-terminal alpha/beta domain (His232 and Asp228) contribute ligands to the catalytic manganese site. Together with a water or hydroxide ion (OH(x)) a five-coordinated trigonal bipyramidal geometry is formed, with OH(x) and His90 forming the axial ligands and manganese shifted out of the equatorial plane in the direction of OH(x). The ligands including OH(x) are tightly constrained by hydrogen bonding with surrounding residues either from the same monomer (Tyr98, Asn144, Trp194, Gln213, Val229, Trp230) or from the neighbouring subunit (Glu231, Tyr235). This underlines the important role of the symmetric dimeric structure of MnSODs in contributing elements to both the active site and the substrate funnel. The Mn cdots, three dots, centered Mn distance (18.4A) is bridged by the hydrogen-bonded His232 of one monomer with Glu231 of the other monomer. A detailed discussion of the structure, a comparison with known structures of soluble MnSODs as well as a model of the cyanobacterial membrane-bound MnSOD is presented.

Crystallization and preliminary crystallographic analysis of manganese superoxide dismutase from Bacillus halodenitrificans

Manganese superoxide dismutase (GP-MnSOD), a component of the so-called 'green protein' (green protein complex) from the facultative anaerobic halodenitrifier Bacillus halodenitrificans, has been crystallized using the hanging-drop vapor diffusion method. Crystals have unit-cell parameters a=b=93.4 A, c=65.0 A, and belong to the space group P4(3)2(1)2. Preliminary analysis indicates there is one monomer in each asymmetric unit. The structural information from this enzyme will enrich our knowledge on its high catalytic activity and its possible role in green protein complex.

Catalytic pathway of manganese superoxide dismutase by direct observation of superoxide

Measurement of catalysis by MnSOD using direct observation of the UV absorbance of superoxide allows determination of steady-state catalytic constants. Stabilizing superoxide in aprotic solvents such as dimethyl sulfoxide permits the use of stopped-flow spectrophotometry, although significant information is lost in the 2- to 4-msec mixing time; generating superoxide by pulse radiolysis requires no mixing time. Studies show that kcat/Km for the decay of superoxide catalyzed by MnSOD proceeds at diffusion control. Investigations using solvent hydrogen isotope effects and enhancement of catalysis by exogenous proton donors show that kcat near 10(4) sec-1 contains a significant contribution from proton transfer steps. The active site of MnSOD is dominated by a hydrogen bond network comprising the manganese-bound aqueous ligand, the side chains of four residues (Gln-143, Tyr-34, His-30, and Tyr-166 from an adjacent subunit), as well as other water molecules. Interrupting this hydrogen bond network by conservative replacement of residues 30, 34, and 166 causes a 10- to 40-fold decrease in maximal velocity, interpreted as an effect on proton transport to the active site, with smaller effects on kcat/Km. Replacement of Gln-143 causes a much greater decrease in catalytic activity, by two to three orders of magnitude, and causes significant changes to the redox potential as well. During catalysis, MnSOD is inhibited by a peroxide complex of the metal in the active site, different from the inhibition of FeSOD and Cu,ZnSOD by Fenton chemistry. Site-specific mutagenesis of active-site residues alters the extent of product inhibition of MnSOD as well, indicating that this is not only a property of the metal. The replacement of Trp-161 with phenylalanine results in a variant that is completely blocked in catalysis by product inhibition.

Second-sphere contributions to substrate-analogue binding in iron(III) superoxide dismutase

A combination of spectroscopic and computational methods has been employed to explore the nature of the yellow and pink low-temperature azide adducts of iron(III) superoxide dismutase (N(3)-FeSOD), which have been known for more than two decades. Variable-temperature variable-field magnetic circular dichroism (MCD) data suggest that both species possess similar ferric centers with a single azide ligand bound, contradicting previous proposals invoking two azide ligands in the pink form. Complementary data obtained on the azide complex of the Q69E FeSOD mutant reveal that relatively minor perturbations in the metal-center environment are sufficient to produce significant spectral changes; the Q69E N(3)-FeSOD species is red in color at all temperatures. Resonance Raman (RR) spectra of the wild-type and Q69E mutant N(3)-FeSOD complexes are consistent with similar Fe-N(3) units in all three species; however, variations in energies and relative intensities of the RR features associated with this unit reveal subtle differences in (N(3)(-))-Fe(3+) bonding. To understand these differences on a quantitative level, density functional theory and semiempirical INDO/S-CI calculations have been performed on N(3)-FeSOD models. These computations support our model that a single azide ligand is present in all three N(3)-FeSOD adducts and suggest that their different appearances reflect differences in the Fe-N-N bond angle. A 10 degrees increase in the Fe-N-N bond angle is sufficient to account for the spectral differences between the yellow and pink wild-type N(3)-FeSOD species. We show that this bond angle is strongly affected by the second coordination sphere, which therefore might also play an important role in orienting incoming substrate for reaction with the FeSOD active site.

Isolation of monomeric Mn(III/II)-H and Mn(III)-complexes from water: evaluation of O-H bond dissociation energies

The syntheses and properties of the monomeric [MnIII/IIH31(OH)]-/2- and [MnIIIH31(O)]2- complexes are reported, where [H31]3- is the tripodal ligand tris[(N'-tert-butylureaylato)-N-ethyl)]aminato. Isotope-labeling studies with H218O confirmed that water is the source of the terminal oxo and oxygen in the hydroxo ligand. The molecular structures of the [MnIIH31(OH)]2- and [MnIIIH31(O)]2- complexes were determined by X-ray diffraction methods and show that each complex has trigonal bipyramidal coordination geometry. The MnIII-O distance in [MnIIIH31(O)]2- is 1.771(4) A, which is lengthened to 2.059(2) A in [MnIIH31(OH)]2-. Structural studies also show that [H31]3- provides a hydrogen-bond cavity that surrounds the MnIII-O(H) units. Using a thermodynamic approach, which requires pKa and redox potentials, bond dissociation energies of 77(4) and 110(4) kcal/mol were calculated for [MnIIH31(O-H)]2- and [MnIIIH31(O-H)]-, respectively. The calculated value of 77 kcal/mol for the [MnIIH31(O-H)]2- complex is supported by the ability of [MnIIIH31(O)]2- complex to cleave C-H bonds with bond energies of <80 kcal/mol.

Comparison of the crystal structures of the human manganese superoxide dismutase and the homologous Aspergillus fumigatus allergen at 2-A resolution

Manganese superoxide dismutase (MnSOD) of Aspergillus fumigatus, a fungus involved in many pulmonary complications, has been identified as IgE-binding protein. It has been shown also that MnSODs from other organisms, including human, are recognized by IgE Abs from individuals sensitized to A. fumigatus MnSOD. Comparison of the fungal and the human crystal structure should allow the identification of structural similarities responsible for IgE-mediated cross-reactivity. The three-dimensional structure of A. fumigatus MnSOD has been determined at 2-A resolution by x-ray diffraction analysis. Crystals belonged to space group P2(1)2(1)2(1) with unit cell dimensions of a = 65.88 A, b = 98.7 A, and c = 139.28 A. The structure was solved by molecular replacement using the structure of the human MnSOD as a search model. The final refined model included four chains of 199-200 amino acids, four manganese ions, and 745 water molecules, with a crystallographic R-factor of 19.4% and a free R-factor of 23.3%. Like MnSODs of other eukaryotic organisms, A. fumigatus MnSOD forms a homotetramer with the manganese ions coordinated by three histidines, one aspartic acid, and one water molecule. The fungal and the human MnSOD share high similarity on the level of both primary and tertiary structure. We identified conserved amino acids that are solvent exposed in the fungal and the human crystal structure and are therefore potentially involved in IgE-mediated cross-reactivity.

Coupled redox potentials in manganese and iron superoxide dismutases from reaction kinetics and density functional/electrostatics calculations

A methodology for determining the coupled redox potentials (DeltaE(redox) degrees (coupled)) of manganese and iron superoxide dismutases (Mn(Fe)SODs), from the standard redox potential of reaction (O(2)(-) + 2H(+) + e(-) --> H(2)O(2)) and the experimental kinetic rate constants of Mn(Fe)SOD proteins, has been presented for the first time. A combined density functional (DF) and electrostatic protein/reaction field (DF/electrostatics) model has also been applied to seven protein structures, to study the structural, energetic, simple redox potential, pK(a), and coupled redox potential properties associated with each active site. The quantum cluster active site models, which include the metal, first shell ligands, represented by amino acid side chains and a solvent derived ligand, and the second shell H-bonding partners, were taken from the crystal structures, and geometry was optimized in four kinds of states: oxidized (III) and reduced (II) states with either a H(2)O molecule or a OH(-) group as the fifth coordinated ligand. We conclude from the calculations that the oxidized and reduced Mn(Fe)SODs are in the Mn(3+)(Fe(3+))(OH(-)) and Mn(2+)(Fe(2+))(H(2)O) forms, respectively; proton transfers will happen in both steps of the dismutation of superoxide anion (O(2)(-)), and the proton-transfer reactions will occur prior to or concerted with the electron transfer from O(2)(-) group to the Mn(3+)(Fe(3+))SOD metal center. The DeltaE(redox) degrees (coupled) of E. coli FeSOD calculated by the DF/electrostatics method is 0.16 V, which is very close to the experimental value of 0.25 V. The absolute values of DeltaE(redox) degrees (coupled) for T. thermophilus, human wild-type, and mutant Q143N MnSODs obtained from the DF/electrostatics method are -0.25, -0.29, and -0.11 V, which present the same trend and very similar relative values to those obtained from experimental kinetic rate constants (0.40, 0.32, and 0.59 V, respectively). The order DeltaE(redox) degrees (human wild-type) < DeltaE(redox) degrees (T. thermophilus) < DeltaE(redox) degrees (E. coli) < DeltaE(redox) degrees (Q143N) for MnSOD proteins is predicted by the DF/electrostatics calculations.

Engineering of an intersubunit disulfide bridge in the iron-superoxide dismutase of Mycobacterium tuberculosis

With the aim of enhancing interactions involved in dimer formation, an intersubunit disulfide bridge was engineered in the superoxide dismutase enzyme of Mycobacterium tuberculosis. Ser-123 was chosen for mutation to cysteine since it resides at the dimer interface where the serine side chain interacts with the same residue in the opposite subunit. Gel electrophoresis and X-ray crystallographic studies of the expressed mutant confirmed formation of the disulfide bond under nonreducing conditions. However, the mutant protein was found to be less stable than the wild type as judged by susceptibility to denaturation in the presence of guanidine hydrochloride. Decreased stability probably results from formation of a disulfide bridge with a suboptimal torsion angle and exclusion of solvent molecules from the dimer interface.

Crystal structure of manganese catalase from Lactobacillus plantarum

BACKGROUND

Catalases are important antioxidant metalloenzymes that catalyze disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and the other, a structurally distinct family containing nonheme manganese. We have solved the structure of the mesophilic manganese catalase from Lactobacillus plantarum and its azide-inhibited complex.

RESULTS

The crystal structure of the native enzyme has been solved at 1.8 A resolution by molecular replacement, and the azide complex of the native protein has been solved at 1.4 A resolution. The hexameric structure of the holoenzyme is stabilized by extensive intersubunit contacts, including a beta zipper and a structural calcium ion crosslinking neighboring subunits. Each subunit contains a dimanganese active site, accessed by a single substrate channel lined by charged residues. The manganese ions are linked by a mu1,3-bridging glutamate carboxylate and two mu-bridging solvent oxygens that electronically couple the metal centers. The active site region includes two residues (Arg147 and Glu178) that appear to be unique to the Lactobacillus plantarum catalase.

CONCLUSIONS

A comparison of L. plantarum and T. thermophilus catalase structures reveals the existence of two distinct structural classes, differing in monomer design and the organization of their active sites, within the manganese catalase family. These differences have important implications for catalysis and may reflect distinct biological functions for the two enzymes, with the L. plantarum enzyme serving as a catalase, while the T. thermophilus enzyme may function as a catalase/peroxidase.

Removing a hydrogen bond in the dimer interface of Escherichia coli manganese superoxide dismutase alters structure and reactivity

Among manganese superoxide dismutases, residues His30 and Tyr174 are highly conserved, forming part of the substrate access funnel in the active site. These two residues are structurally linked by a strong hydrogen bond between His30 NE2 from one subunit and Tyr174 OH from the other subunit of the dimer, forming an important element that bridges the dimer interface. Mutation of either His30 or Tyr174 in Escherichia coli MnSOD reduces the superoxide dismutase activity to 30--40% of that of the wt enzyme, which is surprising, since Y174 is quite remote from the active site metal center. The 2.2 A resolution X-ray structure of H30A-MnSOD shows that removing the Tyr174-->His30 hydrogen bond from the acceptor side results in a significant displacement of the main-chain segment containing the Y174 residue, with local rearrangement of the protein. The 1.35 A resolution structure of Y174F-MnSOD shows that disruption of the same hydrogen bond from the donor side has much greater consequences, with reorientation of F174 having a domino effect on the neighboring residues, resulting in a major rearrangement of the dimer interface and flipping of the His30 ring. Spectroscopic studies on H30A, H30N, and Y174F mutants show that (like the previously characterized Y34F mutant of E. coli MnSOD) all lack the high pH transition of the wt enzyme. This observation supports assignment of the pH sensitivity of MnSOD to coordination of hydroxide ion at high pH rather than to ionization of the phenolic group of Y34. Thus, mutations near the active site, as in the Y34F mutant, as well as at remote positions, as in Y174F, similarly affect the metal reactivity and alter the effective pK(a) for hydroxide ion binding. These results imply that hydrogen bonding of the H30 imidazole N--H group plays a key role in substrate binding and catalysis.

Topologically constrained manganese(III) and iron(III) complexes of two cross-bridged tetraazamacrocycles

A family of Mn3+ and Fe3+ complexes of 4,11-dimethyl-1,4,8,11-tetraazabicyclo[6.6.2]hexadecane (1) and 4,10-dimethyl-1,4,7,10-tetraazabicyclo[5.5.2]tetradecane (2) has been prepared by the chemical oxidation of the divalent manganese and iron analogues. The ligands are ethylene cross-bridged tetraazamacrocycles derived from cylam and cyclen, respectively. The synthesis and characterization of these complexes, including X-ray crystal structure determinations, are described. The structural evidence demonstrates that the tetradentate ligands enforce distorted octahedral geometries on the metal ions, with two cis sites occupied by labile ligands. Magnetic measurements reveal that the complexes are high spin with typical magnetic moments. Cyclic voltammetry shows reversible redox processes for the Fe3+/Fe2+ couples of the iron(III) complexes, while Mn3+/Mn2+ and Mn4+/Mn3+ couples were observed for the complexes with manganese(III). The manganese chemistry of 1 was studied in depth. The dichloro manganese(III) cation of 1 undergoes facile ligand substitution reactions at the labile, monodentate sites, for example substituting azide for chloride ligands. Air oxidation of the dichloro complex of Mn (1)2+ in basic solution does not give the expected mu-oxo dimeric product common to manganese. Instead, an unusual manganese(III)-OH complex has been isolated from this reaction and structurally characterized. A similar reaction under slightly different conditions gives a putative MnIII(OH)2 complex that metathesizes to MnIII(OMe)2 upon recrystallization from methanol.

Outer sphere mutations perturb metal reactivity in manganese superoxide dismutase

Tyrosine 34 and glutamine 146 are highly conserved outer sphere residues in the mononuclear manganese active site of Escherichia coli manganese superoxide dismutase. Biochemical and spectroscopic characterization of site-directed mutants has allowed functional characterization of these residues in the wild-type (wt) enzyme. X-ray crystallographic analysis of three mutants (Y34F, Q146L, and Q146H) reveal subtle changes in the protein structures. The Y34A mutant, as well as the previously reported Y34F mutant, retained essentially the full superoxide dismutase activity of the wild-type enzyme, and the X-ray crystal structure of Y34F manganese superoxide dismutase shows that mutation of this strictly conserved residue has only minor effects on the positions of active site residues and the organized water in the substrate access funnel. Mutation of the outer sphere solvent pocket residue Q146 has more dramatic effects. The Q146E mutant is isolated as an apoprotein lacking dismutase activity. Q146L and Q146H mutants retain only 5-10% of the dismutase activity of the wild-type enzyme. The absorption and circular dichroism spectra of the Q146H mutant resemble corresponding data for the superoxide dismutase from a hyperthermophilic archaeon, Pyrobaculum aerophilum, which is active in both Mn and Fe forms. Interestingly, the iron-substituted Q146H protein also exhibits low dismutase activity, which increases at lower pH. Mutation of glutamine 146 disrupts the hydrogen-bonding network in the active site and has a greater effect on protein structure than does the Y34F mutant, with rearrangement of the tyrosine 34 and tryptophan 128 side chains.

The hyper-thermostable Fe-superoxide dismutase from the Archaeon Acidianus ambivalens: characterization, recombinant expression, crystallization and effects of metal exchange

An iron-containing superoxide dismutase (SOD; EC 1.15.1.1) of the hyperthermophilic archaeon Acidianus ambivalens (Aa-SOD) has been purified and characterized and the gene has been cloned and sequenced. The SOD from the facultatively aerobic member of the crenarchaeota could be expressed in E. coli. Both, the native as well as the heterologously overproduced protein turned out to have extraordinarily high melting temperatures of 128 degrees C and 124.5 degrees C, respectively. To the best of our knowledge, this is the highest directly measured melting temperature of a native protein. Surprisingly, neither the native nor the recombinant superoxide dismutase displays 100% occupation of the metal coordination sites. Obviously it is not the incorporation of a metal ion that confers the extreme thermostability. Expression of the superoxide dismutase in the presence of different metals such as Fe, Co, Ni, Mn and Cu offered the possibility of studying the hitherto unknown cofactor preference of iron-superoxide dismutase. The recombinant enzyme displayed the highest preference for incorporation of cobalt although iron is used as the natural cofactor. Spectroscopic analysis by EPR, atomic absorption and UVNis spectroscopy as well as activity measurements and differential scanning calorimetry of the metal substituted superoxide dismutases were performed. However, the superoxide dismutase of A. ambivalens is active only with iron but may incorporate other metals equally well in the catalytic center without loss of conformational stability or heat tolerance. The co-form of the enzyme could be crystallized.

Crystal structure of cambialistic superoxide dismutase from porphyromonas gingivalis

The crystal structure of cambialistic superoxide dismutase (SOD) from Porphyromonas gingivalis, which exhibits full activity with either Fe or Mn at the active site, has been determined at 1.8-A resolution by molecular replacement and refined to a crystallographic R factor of 17.9% (Rfree 22.3%). The crystals belong to the space group P212121 (a = 75.5 A, b = 102.7 A, c = 99.6 A) with four identical subunits in the asymmetric unit. Each pair of subunits forms a compact dimer, but not a tetramer, with 222 point symmetry. Each subunit has 191 amino-acid residues most of which are visible in electron density maps, and consists of seven alpha helices and one three-stranded antiparallel beta sheet. The metal ion, a 3 : 1 mixture of Fe and Mn, is coordinated with five ligands (His27, His74, His161, Asp157, and water) arranged at the vertices of a trigonal bipyramid. Although the overall structural features, including the metal coordination geometry, are similar to those found in other single-metal containing SODs, P. gingivalis SOD more closely resembles the dimeric Fe-SODs from Escherichia coli rather than another cambialistic SOD from Propionibacterium shermanii, which itself is rather similar to other tetrameric SODs.

Structures of the superoxide reductase from Pyrococcus furiosus in the oxidized and reduced states

Superoxide reductase (SOR) is a blue non-heme iron protein that functions in anaerobic microbes as a defense mechanism against reactive oxygen species by catalyzing the reduction of superoxide to hydrogen peroxide [Jenney, F. E., Jr., Verhagen, M. F. J. M., Cui, X. , and Adams, M. W. W. (1999) Science 286, 306-309]. Crystal structures of SOR from the hyperthermophilic archaeon Pyrococcus furiosus have been determined in the oxidized and reduced forms to resolutions of 1.7 and 2.0 A, respectively. SOR forms a homotetramer, with each subunit adopting an immunoglobulin-like beta-barrel fold that coordinates a mononuclear, non-heme iron center. The protein fold and metal center are similar to those observed previously for the homologous protein desulfoferrodoxin from Desulfovibrio desulfuricans [Coelho, A. V., Matias, P., Fülöp, V., Thompson, A., Gonzalez, A., and Carrondo, M. A. (1997) J. Bioinorg. Chem. 2, 680-689]. Each iron is coordinated to imidazole nitrogens of four histidines in a planar arrangement, with a cysteine ligand occupying an axial position normal to this plane. In two of the subunits of the oxidized structure, a glutamate carboxylate serves as the sixth ligand to form an overall six-coordinate, octahedral coordinate environment. In the remaining two subunits, the sixth coordination site is either vacant or occupied by solvent molecules. The iron centers in all four subunits of the reduced structure exhibit pentacoordination. The structures of the oxidized and reduced forms of SOR suggest a mechanism by which superoxide accessibility may be controlled and define a possible binding site for rubredoxin, the likely physiological electron donor to SOR.

Cryo-trapping the six-coordinate, distorted-octahedral active site of manganese superoxide dismutase

Superoxide dismutase protects organisms from potentially damaging oxygen radicals by catalyzing the disproportionation of superoxide to oxygen and hydrogen peroxide. We report the use of cryogenic temperatures to kinetically capture the sixth ligand bound to the active site of manganese superoxide dismutase (MnSOD). Synchrotron X-ray diffraction data was collected from Escherichia coli MnSOD crystals grown at pH 8.5 and cryocooled to 100 K. Structural refinement to 1.55 A resolution and close inspection of the active site revealed electron density for a sixth ligand that was interpreted to be a hydroxide ligand. The six-coordinate, distorted-octahedral geometry assumed during inhibition by hydroxide is compared to the room temperature, five-coordinate, trigonal bipyramidal active site determined with crystals grown from practically identical conditions. The gateway residues Tyr34, His30 and a tightly bound water molecule are implicated in closing-off the active site and blocking the escape route of the sixth ligand.