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Catalysis research of relevance to carbon management: progress, challenges, and opportunities.

The goal of the "Opportunities for Catalysis Research in Carbon Management" workshop was to review within the context of greenhouse gas/carbon issues the current state of knowledge, barriers to further scientific and technological progress, and basic scientific research needs in the areas of H2 generation and utilization, light hydrocarbon activation and utilization, carbon dioxide activation, utilization, and sequestration, emerging techniques and research directions in relevant catalysis research, and in catalysis for more efficient transportation engines. Several overarching themes emerge from this review. First and foremost, there is a pressing need to better understand in detail the catalytic mechanisms involved in almost every process area mentioned above. This includes the structures, energetics, lifetimes, and reactivities of the species thought to be important in the key catalytic cycles. As much of this type of information as is possible to acquire would also greatly aid in better understanding perplexing, incomplete/inefficient catalytic cycles and in inventing new, efficient ones. The most productive way to attack such problems must include long-term, in-depth fundamental studies of both commercial and model processes, by conventional research techniques and, importantly, by applying various promising new physicochemical and computational approaches which would allow incisive, in situ elucidation of reaction pathways. There is also a consensus that more exploratory experiments, especially high-risk, unconventional catalytic and model studies, should be undertaken. Such an effort will likely require specialized equipment, instrumentation, and computational facilities. The most expeditious and cost-effective means to carry out this research would be by close coupling of academic, industrial, and national laboratory catalysis efforts worldwide. Completely new research approaches should be vigorously explored, ranging from novel compositions, fabrication techniques, reactors, and reaction conditions for heterogeneous catalysts, to novel ligands and ligation geometries (e.g., biomimetic), reaction media, and activation methods for homogeneous ones. The interplay between these two areas involving various hybrid and single-site supported catalyst systems should also be productive. Finally, new combinatorial and semicombinatorial means to rapidly create and screen catalyst systems are now available. As a complement to the approaches noted above, these techniques promise to greatly accelerate catalyst discovery, evaluation, and understanding. They should be incorporated in the vigorous international research effort needed in this field.

Journal Article↗

O-GlcNAcase catalyzes cleavage of thioglycosides without general acid catalysis.

O-GlcNAcase catalyzes the removal of N-acetylglucosamine residues from serine and threonine residues of post-translationally modified proteins using a catalytic mechanism involving substrate-assisted catalysis and general acid/base catalysis. Since thioglycosides are widely perceived as resistant to hydrolysis by glycosidases, it was surprising to find that O-GlcNAcase also catalyzes the efficient hydrolysis of S-glycosides. Brønsted analyses and pH-activity studies of the O-GlcNAcase-catalyzed hydrolysis of a series of aryl S- and O-glycosides reveal that O-GlcNAcase effects hydrolysis of thioglycosides without the assistance of general acid catalysis. alpha-Deuterium kinetic isotope effects for O- and S-glycosides, as well as Taft-like analyses using N-fluoroacetyl-beta-glycosides, suggest that O-GlcNAcase accomplishes hydrolysis of thioglycosides by stabilizing late transition states. For S-glycosides this transition state shows greater nucleophilic participation from the 2-acetamido group than for O-glycosides. The rate constants governing the O-GlcNAcase-catalyzed hydrolysis of O- and S-glycosides as compared to those previously determined for the spontaneous hydrolysis of structurally similar O,O- and O,S-acetals show a similar ratio. O-GlcNAcase therefore demonstrates similar catalytic proficiency toward both O- and S-glycosides. We conclude that O-GlcNAcase is a bifunctional catalyst capable of efficiently cleaving thioglycosides without general acid catalysis, an observation that may have biological implications.

Journal Article↗

Changes in the relative contribution of specific and general base catalysis in cationic micelles. The cyclization of substituted ethyl hydantoates.

The rate-surfactant profiles for the HO(-)- and AcO(-)-catalyzed ring closure of two ethyl hydantoates, E2 and E3, to hydantoins with three cetyltrimethylammonium salts (CTAX, X = Br(-), Cl(-), or AcO(-)) are measured in 0.02 and 0.2 M acetate buffers 50% base with starting pH 4.65. Marked accelerations associated with large pH increases are found in 0.02 M buffered CTAOAc. Smaller accelerations and smaller pH changes are observed in 0.2 M buffered CTAOAc and CTACl. From these profiles, the micellar rate constants for the specific base- and general base-catalyzed reactions, and, respectively, of E2 and E3 are obtained separately. The resulting values of k(2,m)/k(w), E2/E3 rate constant ratios, and kinetic solvent isotope effects, KSIEs, are consistent with a strong predominance of the HO(-) reaction in the dilute buffer, while in the more concentrated buffer, specific and general catalysis compete for the two substrates. This result is in sharp contrast with that observed in water in which the reaction of E2 is almost exclusively specifically catalyzed. The increase in the general base-catalyzed pathway for E2 is attributed not to an increase in the rate constant for this pathway in micelles but to a smaller decrease than that for the specific catalysis (k(2,m)/k(w) = 0.2 and 0.4 for the specific and general catalysis, respectively). The different responses of the rate constants to the micellar media are interpreted as a larger effect of the interfacial polarity on the specific than on the general catalysis. The apparent contradiction between the rate constant decreases and the marked accelerations in micellar media is discussed in terms of pH changes, i.e., [HO(-)] changes, and of acetate inclusion via ion exchanges at micellar interfaces.

Journal Article↗

Advanced chemical design with supported metal complexes for selective catalysis.

This review covers several recent topics of novel catalyst design with supported metal complexes on oxide surfaces for selective catalysis such as chiral self-dimerization to create asymmetric oxidative coupling catalysis, surface functionalization with achiral reagents to promote asymmetric catalysis, and molecular imprinting to design shape-selective catalysis. The new concepts and designs find wide applications to a variety of selective catalysts.

Journal Article↗

Pyruvate carboxylase from a thermophilic Bacillus. Studies on the specificity of activation by acyl derivatives of coenzyme A and on the properties of catalysis in the absence of activator.

1. Oxaloacetate synthesis catalysed by pyruvate carboxylase from a thermophilic Bacillus in the absence of acetyl-CoA required addition of high concentrations of pyruvate, MgATP(2-) and HCO(3) (-), and at 45 degrees C occurred at a maximum rate approx. 20% of that in the presence of a saturating concentration of acetyl-CoA. The apparent K(m) for HCO(3) (-) at pH7.8 was 400mm without acetyl-CoA, and 16mm with a saturating activator concentration. The relationship between reciprocal initial rate and reciprocal MgATP(2-) concentration was non-linear (convex-down) in the absence of acetyl-CoA, but the extent of deviation decreased as the activator concentration was increased. The relationship between reciprocal initial rate and reciprocal pyruvate concentration was non-linear (convex-down) in the presence or absence of acetyl-CoA. 2. The optimum pH for catalysis of oxaloacetate synthesis was similar in the presence or absence of acetyl-CoA. The variation with pH of apparent K(m) for HCO(3) (-) implicated residue(s) with pK(a) 8.6 in catalysis of the activator-independent oxaloacetate synthesis. 3. Linear Arrhenius and van't Hoff plots were observed for the temperature-dependence of oxaloacetate synthesis in the absence of acetyl-CoA over the range 25-55 degrees C. E(a) (activation energy) was 56.3kJ/mol and DeltaH(double dagger) (HCO(3) (-)) (enthalpy of activation) was -38.6kJ/mol. In the presence of acetyl-CoA, biphasic Arrhenius and van't Hoff plots are observed with a change of slope at 30 degrees C in each case. E(a) was 43.7 and 106.3kJ/mol above and below 30 degrees C respectively. 4. Incubation of Bacillus pyruvate carboxylase with trinitrobenzenesulphonate caused specific inactivation of acetyl-CoA-dependent catalytic activity associated with the incorporation of 1.3+/-0.2 trinitrophenyl residues per subunit. Activator-independent catalysis and regulatory inhibition by l-aspartate were unaffected. The rate of inactivation of acetyl-CoA-dependent catalysis by trinitrobenzenesulphonate was specifically decreased by addition of acetyl-CoA and other acetyl-CoA and other acyl-CoA species, but complete protection was not obtained. 5. All alkylacyl derivatives of CoA tested activated Bacillus pyruvate carboxylase; acetyl-CoA was the most effective. The apparent K(a) exhibited a biphasic relationship with acyl-chain length for the straight-chain homologues. Certain long-chain acyl-CoA species showed additional activation at a high concentration. Weak activation occurred on addition of CoA or adenosine 3',5'-bisphosphate, but carboxyacyl-CoA species and derivatives containing a modified phosphoadenosyl group were inhibitory. Thioesters of CoA with non-carboxylic acids, e.g. methanesulphonyl-CoA, serve as activators of the thermophilic Bacillus and Saccharomyces cerevisiae pyruvate carboxylases, but as inhibitors of pyruvate carboxylases obtained from chicken and rat liver. 6. alpha-Oxoglutarate mimics the effect of l-aspartate as a regulatory inhibitor of the pyruvate carboxylases from both the thermophilic Bacillus and Saccharomyces cerevisiae. l-Glutamate was ineffective in both cases.

Acetyl Coenzyme A↗

Effects of transition metals on nitric oxide synthase catalysis.

The biosynthesis of nitric oxide (NO) by the enzyme NO synthase (NOS) proceeds by the hydroxylation of L-arginine to form NG-hydroxy-L-arginine followed by the conversion of NG-hydroxy-L-arginine to L-citrulline and NO. The previously identified requirements of this relatively complicated reaction include several protein-bound cofactors: cytochrome P450-type heme, flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), and tetrahydrobiopterin (H4B). In addition to L-arginine, NOS also requires the substrates NADPH and molecular oxygen. The role of H4B in NOS catalysis has long been a subject of debate and uncertainty fueled, in part, by the failure to detect any dependence of the NOS reaction on nonheme iron, a cofactor integral to catalysis in every other H4B-dependent enzyme. Here we report the ability of NOS to bind transition metals stoichiometrically, and demonstrate that the rate of catalysis is enhanced by nonheme iron. We also show that other divalent transition metals, including Cu, Zn, Co, and Ni, inhibit NOS catalysis. Also, the addition of Cu2+ to NOS inhibits heme reduction, whereas the addition of Fe2+ does not. Overall, the results appear to connect NOS to the known H4B/nonheme iron-dependent hydroxylases, and suggest a similar, if not identical, step in the NOS reaction mechanism.

Animals↗

Tetrahydrobiopterin inhibits monomerization and is consumed during catalysis in neuronal NO synthase.

The biosynthesis of nitric oxide (NO) is catalyzed by homodimeric NO synthases (NOS). For unknown reasons, all NOS co-purify with substoichiometric amounts of (6R)-5,6,7,8-tetrahydrobiopterin (H(4)Bip) and require additional H(4)Bip for maximal activity. We examined the effects of H(4)Bip and pterin-derived inhibitors (anti-pterins) on purified neuronal NOS-I quaternary structure and H(4)Bip content. During L-arginine turnover, NOS-I dimers time dependently dissociated into inactive monomers, paralleled by a loss of enzyme-associated pterin. Dimer dissociation was inhibited when saturating levels of H(4)Bip were added during catalysis. Similar results were obtained with pterin-free NOS-I expressed in Escherichia coli. This stabilizing effect of H(4)Bip was mimicked by the anti-pterin 2-amino-4,6-dioxo-3,4,5,6,8,8a,9, 10-octahydro-oxazolo[1,2f]-pteridine (PHS-32), which also displaced NOS-associated H(4)Bip in a competitive manner. Surprisingly, H(4)Bip not only dissociated from NOS during catalysis, but was only partially recovered in the solute (50.0 +/- 16.5% of control at 20 min). NOS-associated H(4)Bip appeared to react with a NOS catalysis product to a derivative distinct from dihydrobiopterin or biopterin. Under identical conditions, reagent H(4)Bip was chemically stable and fully recovered (95.5 +/- 3.4% of control). A similar loss of both reagent and enzyme-bound H(4)Bip and dimer content was observed by NO generated from spermine NONOate. In conclusion, we propose a role for H(4)Bip as a dimer-stabilizing factor of neuronal NOS during catalysis, possibly by interfering with enzyme destabilizing products.

Arginine↗

Mutational analysis of a Ser/Thr phosphatase. Identification of residues important in phosphoesterase substrate binding and catalysis.

The Ser/Thr phosphoprotein phosphatases (PPases) display similarities in amino acid sequence and biochemical properties. Most members of this family require transition metal ions for activity. The smallest family member, the bacteriophage lambda PPase (lambda-PPase), has been successfully overexpressed in Escherichia coli, purified, and characterized (Zhuo, S., Clemens, J.C., Hakes, D.J., Barford, D., and Dixon, J. E. (1993) J. Biol. Chem. 268, 17754-17761). Site-directed mutagenesis has now been employed to define amino acid residues in lambda-PPase required for metal ion binding and catalysis. Conservative amino acid substitutions at residues Asp20, His22, Asp49, His76, and Glu77 affected lambda-PPase catalysis and metal ion binding, whereas substitutions at residues Arg53 and Arg73 affected catalysis and substrate binding. Each of these residues is invariant in all phosphoprotein phosphatases, suggesting that these residues may play important roles in binding and catalysis in all of the PPases. Computer-assisted sequence alignment further revealed that lambda-PPase residues Asp20, His22, Asp49, His76, Arg53, and Arg73 lie within three larger regions of PPase sequence identity with the consensus sequence (DXH-(approximately 25)-GDXXD-(approximately 25)-GNHD/E). This motif can be found in a wide variety of phosphoesterases unrelated to the PPases and defines structural and catalytic features utilized by a diverse group of enzymes for the hydrolysis of phosphate esters.

Amino Acid Sequence↗

Biotransformation of 13-cis- and 9-cis-retinoic acid to all-trans-retinoic acid in rat conceptal homogenates. Evidence for catalysis by a conceptal isomerase.

The purpose of this study was to investigate whether and to what extent the steric isomerization of retinoic acids in conceptal tissues can be attributed to enzymatic catalysis in addition to thiol-dependent, nonenzymatic catalysis. Conversions of 13-cis-retinoic acid and 9-cis-retinoic acid to all-trans-retinoic acid catalyzed by cell-free preparations of conceptal rat tissues (gestational day 12.5) were investigated. Substrates and rat conceptal homogenates (RCH) were incubated in sodium phosphate buffer (0.1 M, pH 7.5) at 37 degrees C in the dark. Incubation mixtures were quantitatively analyzed by HPLC. In RCH-catalyzed reactions, conversions of 13-cis-retinoic acid or 9-cis-retinoic acid to all-trans-retinoic acid were very rapid, in comparison with uncatalyzed isomerization reactions (incubations without RCH). Comparisons of the rates of reactions catalyzed by freshly prepared vs. freshly prepared/dialyzed RCH showed no significant differences, indicating that small, suflhydryl-containing molecules such as reduced glutathione did not significantly contribute to the RCH-catalyzed reactions. Furthermore, at physiological concentrations (2.5-10 mM), reduced glutathione exhibited very low specific catalytic activities, indicating that nonenzymatic, sulfhydryl-dependent catalysis was not a major mechanism in catalyzing interconversions of retinoic acids in vivo. Enzymatic catalysis by RCH of the conversion of 13-cis-retinoic acid to all-trans-retinoic acid was further characterized by showing 1) substrate saturation kinetics, 2) reaction rates that increased proportionally with protein concentrations, and (3) much greater sensitivity of the reactions to heat inactivation and denaturation by urea, compared with nonenzymatic, glutathione-catalyzed reactions. Thus, isomerization of retinoids in conceptal tissues appeared to be under enzymatic control.

Alitretinoin↗

Homogeneous Gold Catalysis: Development and Recent Advances.

Gold catalysis has witnessed remarkable advances over the past decade, with numerous insightful reviews chronicling this progress. However, a comprehensive review addressing developments in the field during the post-pandemic COVID era remains notably absent. This review aims to bridge that gap by providing an in-depth analysis of recent studies, shedding light on the unique properties of gold complexes, particularly the intriguing aurophilic interactions that distinguish gold chemistry. The review systematically explores the latest achievements in both mono- and dinuclear gold-catalyzed reactions, with a focus on their applications in diverse fields, including redox coupling, asymmetric catalysis, photo-, and electrocatalysis. A special emphasis is placed on the comparative performance of mono- and dinuclear gold catalysts, with the latter often exhibiting enhanced catalytic efficiency and selectivity in certain reactions. By integrating mechanistic insights and DFT perspectives with representative experimental studies from recent years, this review highlights the significance of gold catalysis to synthetic chemistry, identifies emerging trends and outlines future directions for the field.

Catalysis↗

Artificial metalloenzymes for enantioselective catalysis based on the noncovalent incorporation of organometallic moieties in a host protein.

Enzymatic and homogeneous catalysis offer complementary means to produce enantiopure products. Incorporation of achiral, biotinylated aminodiphosphine-rhodium complexes in (strept)avidin affords enantioselective hydrogenation catalysts. A combined chemogenetic procedure allows the optimization of the activity and the selectivity of such artificial metalloenzymes: the reduction of acetamidoacrylate proceeds to produce N-acetamidoalanine in either 96 % ee (R) or 80 % ee (S). In addition to providing a chiral second coordination sphere and, thus, selectivity to the catalyst, the phenomenon of protein-accelerated catalysis (e.g., increased activity) was unraveled. Such artificial metalloenzymes based on the biotin-avidin technology display features that are reminiscent of both homogeneous and of enzymatic catalysis.

Binding Sites↗

First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine.

We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, approximately 4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies.

Antibodies, Catalytic↗

Enzymatic radical catalysis: coenzyme B12-dependent diol dehydratase.

A peculiar function resides in a peculiar structure. Coenzyme B(12) or adenosylcobalamin, a naturally occurring organometallic compound, serves as a cofactor for enzymatic radical reactions. How do the enzymes form catalytic radicals at the active sites? How do the enzymes utilize and control the high reactivity of the radicals for catalysis? Recently, three-dimensional structures of several radical-containing or radical-forming enzymes including B(12) enzymes have been reported, enabling the analysis of the fine mechanisms of the action of these interesting enzymes. Our biochemical, mutational, and crystallographic studies as well as theoretical calculations on diol dehydratase, an adenosylcobalamin-dependent enzyme, revealed that its structure is adapted for its function-that is, activation of the Cobond;C bond toward homolysis, abstraction of a specific hydrogen atom from the substrate and its recombination to a particular product, and transition state stabilization in the hydroxyl group migration of a substrate-derived radical. The functions of K(+) and the active-site amino acid residues in enzyme catalysis are also investigated. Based on the results, the fine mechanism of the enzyme and the energetic feasibility of enzymatic radical catalysis are described here.

Adenine↗

Decavanadate inhibits catalysis by ribonuclease A.

Pentavalent organo-vanadates have been used extensively to mimic the transition state of phosphoryl group transfer reactions. Here, decavanadate (V(10)O(28)6-) is shown to be an inhibitor of catalysis by bovine pancreatic ribonuclease A (RNase A). Isothermal titration calorimetry shows that the Kd for the RNase A decavanadate complex is 1.4 microM. This value is consistent with kinetic measurements of the inhibition of enzymatic catalysis. The interaction between RNase A and decavanadate has a coulombic component, as the affinity for decavanadate is diminished by NaCl and binding is weaker to variant enzymes in which one (K41A RNase A) or three (K7A/R10A/K66A RNase A) of the cationic residues near the active site have been replaced with alanine. Decavanadate is thus the first oxometalate to be identified as an inhibitor of catalysis by a ribonuclease. Surprisingly, decavanadate binds to RNase A with an affinity similar to that of the pentavalent organo-vanadate, uridine 2',3'-cyclic vanadate.

Animals↗

Effects of terminal deletions in C5 protein on promoting RNase P catalysis.

Deletion derivatives of C5 protein, the protein cofactor of Escherichia coli RNase P, were constructed as soluble MBP (maltose-binding protein) fusion proteins to assess the deletion effects on promoting RNase P catalysis and on binding to M1 RNA, the catalytic subunit of the enzyme. The C5 protein, with large terminal deletions, retained its promoting activity of RNase P catalysis under protein excess conditions in vitro. Some deletion derivatives complemented the temperature sensitive phenotype of E. coli A49 cells carrying the rnpA49 mutation. This ability also suggests that part of the C5 protein is enough to produce the catalytic activity of RNase P in vivo. Both the central conserved region, called the RNR motif, and the C-terminal region are essential for the binding of C5 protein to M1 RNA. Meanwhile, the N-terminal region contributes to promoting RNase P catalysis in ways other than binding to M1 RNA.

Amino Acid Sequence↗

Hymenolepis diminuta: catalysis of transmembrane proton translocation by mitochondrial NADPH-->NAD transhydrogenase.

The mitochondrial, inner-membrane-associated, reversible NADPH-->NAD transhydrogenase of adult Hymenolepis diminuta physiologically couples matrix-localized, NADP-specific "malic" enzyme with NADH-dependent anaerobic electron transport. Employing submitochondrial particles (SMP) as the source of enzyme activity and both spectrophotometric and fluorometric assessments, the present study made evident that in its catalysis of transhydrogenation between NADPH and NAD, the cestode enzyme engages in the concomitant transmembrane translocation of protons. As assessed spectrophotometrically, the catalysis of NADPH-dependent NAD reduction by H. diminuta SMP was stimulated significantly by carbonyl cyanide 3-chlorophenylhydrazone (CCCP), carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP), as well as by the protonophoric anthelmintic, niclosamide. In addition, N,N'-dicyclohexylcarbodiimide (DCCD) markedly diminished SMP-catalyzed hydride ion transfer between NADPH and NAD. The catalysis by SMP of concomitant, transhydrogenase-mediated proton translocation was evaluated more directly via fluorometric assays using 8-anilino-1-napthalenesulfonic acid (ANS) as the probe. These latter evaluations revealed a transhydrogenase-dependent enhancement of ANS fluorescence in accord with an intravesicular accumulation of protons. ANS fluorescence was quenched rapidly when the assay system was supplemented with CCCP, FCCP, or niclosamide. Consistent with the helminth transhydrogenase acting as a proton pump, transhydrogenase-mediated enhanced fluorescence also was inhibited by DCCD. Considered collectively, these data indicated, apparently for the first time for any invertebrate system, that the transhydrogenase, in catalyzing the NADPH-->NAD reaction, acts in the translocation of protons from the matrix to the intermembrane space mitochondrial compartment.

Anilino Naphthalenesulfonates↗

Analysis of conserved basic residues associated with DNA binding (Arg69) and catalysis (Lys76) by the RusA holliday junction resolvase.

Holliday junctions are key intermediates in both homologous recombination and DNA repair, and are also formed from replication forks stalled at lesions in the template strands. Their resolution is critical for chromosome segregation and cell viability, and is mediated by a class of small, homodimeric endonucleases that bind the structure and cleave the DNA. All the enzymes studied require divalent metal ions for strand cleavage and their active centres are characterised by conserved aspartate/glutamate residues that provide ligands for metal binding. Sequence alignments reveal that they also contain a number of conserved basic residues. We used site-directed mutagenesis to investigate such residues in the RusA resolvase. RusA is a 120 amino acid residue polypeptide that can be activated in Escherichia coli to promote recombination and repair in the absence of the Ruv proteins. The RuvA, RuvB and RuvC proteins form a complex on Holliday junction DNA that drives coupled branch migration (RuvAB) and resolution (RuvC) reactions. In contrast to RuvC, the RusA resolvase does not interact directly with a branch migration motor, which simplifies analysis of its resolution activity. Catalysis depends on three highly conserved acidic residues (Asp70, Asp72 and Asp91) that define the catalytic centre. We show that Lys76, which is invariant in RusA sequences, is essential for catalysis, but not for DNA binding, and that an invariant asparagine residue (Asn73) is required for optimal activity. Analysis of DNA binding revealed that RusA may interact with one face of an open junction before manipulating its conformation in the presence of Mg(2+) as part of the catalytic process. A well-conserved arginine residue (Arg69) is linked with this critical stage. These findings provide the first insights into the roles played by basic residues in DNA binding and catalysis by a Holliday junction resolvase.

Amino Acid Sequence↗

Solution structure of the catalytic domain of gammadelta resolvase. Implications for the mechanism of catalysis.

The site-specific DNA recombinase, gammadelta resolvase, from Escherichia coli catalyzes recombination of res site-containing plasmid DNA to two catenated circular DNA products. The catalytic domain (residues 1-105), lacking a C-terminal dimerization interface, has been constructed and the NMR solution structure of the monomer determined. The RMSD of the NMR conformers for residues 2-92 excluding residues 37-45 and 64-73 is 0.41 A for backbone atoms and 0.88 A for all heavy atoms. The NMR solution structure of the monomeric catalytic domain (residues 1-105) was found to be formed by a four-stranded parallel beta-sheet surrounded by three helices. The catalytic domain (residues 1-105), deficient in the C-terminal dimerization domain, was monomeric at high salt concentration, but displayed unexpected dimerization at lower ionic strength. The unique solution dimerization interface at low ionic strength was mapped by NMR. With respect to previous crystal structures of the dimeric catalytic domain (residues 1-140), differences in the average conformation of active-site residues were found at loop 1 containing the catalytic S10 nucleophile, the beta1 strand containing R8, and at loop 3 containing D67, R68 and R71, which are required for catalysis. The active-site loops display high-frequency and conformational backbone dynamics and are less well defined than the secondary structures. In the solution structure, the D67 side-chain is proximal to the S10 side-chain making the D67 carboxylate group a candidate for activation of S10 through general base catalysis. Four conserved Arg residues can function in the activation of the phosphodiester for nucleophilic attack by the S10 hydroxyl group. A mechanism for covalent catalysis by this class of recombinases is proposed that may be related to dimer interface dissociation.

Amides↗