The sequences classified as genes for various ribulose-1,5-bisphosphate
(RuBP) carboxylase/oxygenase (RuBisCO)-like proteins (RLPs) are widely
distributed among bacteria, archaea, and eukaryota. In the phylogenic tree
constructed with these sequences, RuBisCOs and RLPs are grouped into four
separate clades, forms I-IV. In RuBisCO enzymes encoded by form I, II, and III
sequences, 19 conserved amino acid residues are essential for CO2
fixation; however, 1-11 of these 19 residues are substituted with other amino
acids in form IV RLPs. Among form IV RLPs, the only enzymatic activity
detected to date is a 2,3-diketo-5-methylthiopentyl 1-phosphate (DK-MTP-1-P)
enolase reaction catalyzed by Bacillus subtilis, Microcystis
aeruginosa, and Geobacillus kaustophilus form IV RLPs. RLPs from
Rhodospirillum rubrum, Rhodopseudomonas palustris,
Chlorobium tepidum, and Bordetella bronchiseptica were
inactive in the enolase reaction. DK-MTP-1-P enolase activity of B.
subtilis RLP required Mg2+ for catalysis and, like RuBisCO,
was stimulated by CO2. Four residues that are essential for the
enolization reaction of RuBisCO, Lys175, Lys201,
Asp203, and Glu204, were conserved in RLPs and were
essential for DK-MTP-1-P enolase catalysis. Lys123...
A conventional class I (subclass a or b) ribonucleotide reductase (RNR) employs a tyrosyl radical (Y•) in its R2 subunit for reversible generation of a 3′-hydrogen-abstracting cysteine radical in its R1 subunit by proton-coupled electron transfer (PCET) through a network of aromatic amino acids spanning the two subunits. The class Ic RNR from the human pathogen Chlamydia trachomatis (Ct) uses a MnIV/FeIII cofactor (specifically, the MnIV ion) in place of the Y• for radical initiation. Ct R2 is activated when its MnII/FeII form reacts with O2 to generate a MnIV/FeIV intermediate, which decays by reduction of the FeIV site to the active MnIV/FeIII state. Here we show that the reduction step in this sequence is mediated by residue Y222. Substitution of Y222 with F retards the intrinsic decay of the MnIV/FeIV intermediate by ∼10-fold and diminishes the ability of ascorbate to accelerate the decay by ∼65-fold but has no detectable effect on the catalytic activity of the MnIV/FeIII–R2 product. By contrast, substitution of Y338, the cognate of the subunit interfacial R2 residue in the R1 ⇔ R2 PCET pathway of the conventional class I RNRs [Y356 in Escherichia coli (Ec) R2], has almost no effect on decay of the MnIV/FeIV intermediate but abolishes catalytic activity. Substitution of W51...
The hydrolysis of glucosylceramide by acid β-glucosidase proceeds via a two-step, double displacement mechanism that includes cleavage of the O-β-glucosidic bond, enzyme-glucosylation and, then, enzyme-deglucosylation. Two residues that may impact this cycle are N370 and E235. The N370S mutant enzyme is very common in Gaucher disease type 1 patients. Homology and crystal data predictions suggested that E235 is the acid/base catalyst in the hydrolytic reaction. Here, the roles of N370 and E235 in hydrolysis were explored using mutant proteins with selected amino acid substitutions. Heterologously expressed enzymes were characterized using inhibitors, activators, and alternative substrates to gain insight into the effects on the glucosylation (single turnover) and deglucosylation (transglucosylation) steps in catalysis. Specific substitutions at N370 selectively altered only the glucosylation step whereas N370S altered this and the deglucosylation steps. To provide functional data to support E235 as the acid/base catalyst, progress curves with poor substrates with more acidic leaving groups were used in the presence and absence of azide as an exogenous nucleophile. The restoration of E235G activity to nearly wild-type levels was achieved using azide with 2...
Cytochrome P450 (P450) protein-protein interactions have been observed with
various in vitro systems. It is interesting to note that these interactions
seem to be isoform-dependent, with some combinations producing no effect and
others producing increased or decreased catalytic activity. With some
exceptions, most of the work to date has involved P450s from rabbit, rat, and
other animal species, with few studies including human P450s. In the studies
presented herein, the interactions of two key drug-metabolizing enzymes,
CYP2C9 and CYP2D6, were analyzed in a purified, reconstituted enzyme system
for changes in both substrate-binding affinity and rates of catalysis. In
addition, an extensive study was conducted as to the “order of
mixing” for the reconstituted enzyme system and the impact on the
observations. CYP2D6 coincubation inhibited CYP2C9-mediated
(S)-flurbiprofen metabolism in a protein concentration-dependent
manner. Vmax values were reduced by up to 50%, but no
appreciable effect on Km was observed. Spectral binding
studies revealed a 20-fold increase in the KS of CYP2C9
toward (S)-flurbiprofen in the presence of CYP2D6. CYP2C9
coincubation had no effect on CYP2D6-mediated dextromethorphan
O-demethylation. The order of combination of the proteins (CYP2C9...
(+)-δ-Cadinene synthase (DCS) from Gossypium arboreum (tree cotton) is a sesquiterpene cyclase that catalyzes the cyclization of farnesyl diphosphate in the first committed step of the biosynthesis of gossypol, a phytoalexin that defends the plant from bacterial and fungal pathogens. Here, we report the X-ray crystal structure of unliganded DCS at 2.4 Å resolution and the structure of its complex with three putative Mg2+ ions and the substrate analogue inhibitor 2-fluorofarnesyl diphosphate (2F-FPP) at 2.75 Å resolution. These structures illuminate unusual features that accommodate the trinuclear metal cluster required for substrate binding and catalysis. Like other terpenoid cyclases, DCS contains a characteristic aspartate-rich motif D307DTYD311 on helix D that interacts with Mg2+A and Mg2+C. However, DCS appears to be unique among terpenoid cyclases in that it does not contain the “NSE/DTE” motif on helix H that specifically chelates Mg2+B, which is usually found as the signature sequence (N, D)D(L, I, V)X(S, T)XXXE (boldface indicates Mg2+B ligands). Instead, DCS contains a second aspartate-rich motif, D451DVAE455, that interacts with Mg2+B. In this regard, DCS is more similar to the isoprenoid chain elongation enzyme farnesyl diphosphate synthase...
Photoredox catalysis and organocatalysis represent two powerful fields of molecule activation that have found widespread application in the areas of inorganic and organic chemistry, respectively. We merged these two catalysis fields to solve problems in asymmetric chemical synthesis. Specifically, the enantioselective intermolecular α-alkylation of aldehydes has been accomplished using an interwoven activation pathway that combines both the photoredox catalyst Ru(bpy)3Cl2 (where bpy is 2,2′-bipyridine) and an imidazolidinone organocatalyst. This broadly applicable, yet previously elusive, alkylation reaction is now highly enantioselective and operationally trivial.
Many naturally occurring biopolymers (i.e., proteins, RNA, DNA) owe their unique properties to their well-defined three-dimensional structures. These attributes have inspired the design and synthesis of folded architectures with functions ranging from molecular recognition to asymmetric catalysis. Among these are synthetic oligomeric peptide (“foldamer”) mimics, which can display conformational ordering at short chain lengths. Foldamers, however, have not been explored as platforms for asymmetric catalysis. This report describes a library of synthetic helical “peptoid” oligomers that enable enantioselective transformations at an embedded achiral catalytic center, as illustrated by the oxidative kinetic resolution of 1-phenylethanol. In an investigation aimed at elucidating key structure–function relationships, we have discovered that the enantioselectivity of the catalytic peptoids depends on the handedness of the asymmetric environment derived from the helical scaffold, the position of the catalytic center along the peptoid backbone, and the degree of conformational ordering of the peptoid scaffold. The transfer of chiral information from a folded scaffold can enable the use of a diverse assortment of embedded achiral catalytic centers...
Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with the low computational cost of empirical molecular mechanical (MM) treatment allowing to capture dynamic properties to probe critical atomistic details of enzyme reactions. Catalysis by RNA enzymes (ribozymes) has only recently begun to be addressed with QM/MM approaches and is thus still a field under development. This review surveys methodology as well as recent advances in QM/MM applications to RNA mechanisms, including those of the HDV, hairpin, and hammerhead ribozymes, as well as the ribosome. We compare and correlate QM/MM results with those from QM and/or molecular dynamics (MD) simulations, and discuss scope and limitations with a critical eye on current shortcomings in available methodologies and computer resources. We thus hope to foster mutual appreciation and facilitate collaboration between experimentalists and theorists to jointly advance our understanding of RNA catalysis at an atomistic level.
Phosphatidyl-myo-inositol mannosyltransferase A (PimA) is an essential glycosyltransferase (GT) involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs), which are key components of the mycobacterial cell envelope. PimA is the paradigm of a large family of peripheral membrane-binding GTs for which the molecular mechanism of substrate/membrane recognition and catalysis is still unknown. Strong evidence is provided showing that PimA undergoes significant conformational changes upon substrate binding. Specifically, the binding of the donor GDP-Man triggered an important interdomain rearrangement that stabilized the enzyme and generated the binding site for the acceptor substrate, phosphatidyl-myo-inositol (PI). The interaction of PimA with the β-phosphate of GDP-Man was essential for this conformational change to occur. In contrast, binding of PI had the opposite effect, inducing the formation of a more relaxed complex with PimA. Interestingly, GDP-Man stabilized and PI destabilized PimA by a similar enthalpic amount, suggesting that they formed or disrupted an equivalent number of interactions within the PimA complexes. Furthermore, molecular docking and site-directed mutagenesis experiments provided novel insights into the architecture of the myo-inositol 1-phosphate binding site and the involvement of an essential amphiphatic α-helix in membrane binding. Altogether...
Superoxide dismutase (SOD) enzymes are critical in controlling levels of reactive oxygen species (ROS) that are linked to aging, cancer and neurodegenerative disease. Superoxide (O2 •−) produced during respiration is removed by the product of the SOD2 gene, the homotetrameric manganese superoxide dismutase (MnSOD). Here, we examine the structural and catalytic roles of the highly conserved active-site residue Tyr34, based upon structure-function studies of MnSOD enzymes with mutations at this site. Substitution of Tyr34 with five different amino acids retained the active site protein structure and assembly, but causes a substantial decrease in the catalytic rate constant for the reduction of superoxide. The rate constant for formation of product inhibition complex also decreases but to a much lesser extent, resulting in a net increase in the product inhibition form of the mutant enzymes. Comparisons of crystal structures and catalytic rates also suggest that one mutation, Y34V, interrupts the hydrogen-bonded network, which is associated with a rapid dissociation of the product-inhibited complex. Notably, with three of the Tyr34 mutants we also observe an intermediate in catalysis, which has not been reported previously. Thus, these mutants establish a means to trap a catalytic intermediate that promises to help elucidate the mechanism of catalysis.
The newly discovered SpvC effector protein from Salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a β-elimination mechanism. To understand this unique phosphothreonine lyase catalysis, the dynamics of the enzyme-substrate complex of the SpvC effector is investigated with a 3.2 ns molecular dynamics simulation, which reveals that the phosphorylated peptide substrate is tightly held in the active site by a hydrogen bond network and the lysine general base is positioned for the abstraction of the alpha hydrogen. The catalysis is further modeled with density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31+G(d,p) level of theory. The DFT calculations indicate the reaction proceeds via a single transition state, featuring a concerted proton abstraction from the α carbon by Lys136 and β elimination of the phosphate leaving group. Key kinetic isotopic effects are predicted based on the truncated active-site model.
Decarbonization of the transport system and a transition to a new diversified energy system that is scalable and sustainable, requires a widespread implementation of carbon-neutral fuels. In biomimetic supramolecular nanoreactors for solar-to-fuel conversion, water-splitting catalysts can be coupled to photochemical units to form complex electrochemical nanostructures, based on a systems integration approach and guided by magnetic resonance knowledge of the operating principles of biological photosynthesis, to bridge between long-distance energy transfer on the short time scale of fluorescence, ~10−9 s, and short-distance proton-coupled electron transfer and storage on the much longer time scale of catalysis, ~10−3 s. A modular approach allows for the design of nanostructured optimized topologies with a tunneling bridge for the integration of storage with catalysis and optimization of proton chemical potentials, to mimic proton-coupled electron transfer processes in photosystem II and hydrogenase.
Subunit movements within the H+-ATP synthase from chloroplasts (CF0F1) are investigated during ATP synthesis. The γ-subunit (γCys-322) is covalently labeled with a fluorescence donor (ATTO532). A fluorescence acceptor (adenosine 5′-(β,γ-imino)triphosphate (AMPPNP)-ATTO665) is noncovalently bound to a noncatalytic site at one α-subunit. The labeled CF0F1 is integrated into liposomes, and a transmembrane pH difference is generated by an acid base transition. Single-pair fluorescence resonance energy transfer is measured in freely diffusing proteoliposomes with a confocal two-channel microscope. The fluorescence time traces reveal a repetitive three-step rotation of the γ-subunit relative to the α-subunit during ATP synthesis. Some traces show splitting into sublevels with fluctuations between the sublevels. During catalysis the central stalk interacts, with equal probability, with each αβ-pair. Without catalysis the central stalk interacts with only one specific αβ-pair, and no stepping between FRET levels is observed. Two inactive states of the enzyme are identified: one in the presence of AMPPNP and one in the presence of ADP.
ADP-glucose pyrophosphorylase controls starch synthesis in plants and is an interesting case to study the evolution and differentiation of roles in heteromeric enzymes. It includes two homologous subunits, small (S) and large (L), that originated from a common photosynthetic eukaryotic ancestor. In present day organisms, these subunits became complementary after loss of certain roles in a process described as subfunctionalization. For instance, the potato tuber enzyme has a noncatalytic L subunit that complements an S subunit with suboptimal allosteric properties. To understand the evolution of catalysis and regulation in this family, we artificially synthesized both subunit genes from the unicellular alga Ostreococcus tauri. This is among the most ancient species in the green lineage that diverged from the ancestor of all green plants and algae. After heterologous gene expression, we purified and characterized the proteins. The O. tauri enzyme was not redox-regulated, suggesting that redox regulation of ADP-glucose pyrophosphorylases appeared later in evolution. The S subunit had a typical low apparent affinity for the activator 3-phosphoglycerate, but it was atypically defective in the catalytic efficiency (Vmax/Km) for the substrate Glc-1-P. The L subunit needed the S subunit for soluble expression. In the presence of a mutated S subunit (to avoid interference)...
4′-Phosphopantetheinyl transferases (PPTs) catalyze the transfer of 4′-phosphopantetheine (4-PP) from coenzyme A to a conserved serine residue of their protein substrates. In humans, the number of pathways utilizing the 4-PP post-translational modification is limited and may only require a single broad specificity PPT for all phosphopantetheinylation reactions. Recently, we have shown that one of the enzymes of folate metabolism, 10-formyltetrahydrofolate dehydrogenase (FDH), requires a 4-PP prosthetic group for catalysis. This moiety acts as a swinging arm to couple the activities of the two catalytic domains of FDH and allows the conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. In the current study, we demonstrate that the broad specificity human PPT converts apo-FDH to holoenzyme and thus activates FDH catalysis. Silencing PPT by small interfering RNA in A549 cells prevents FDH modification, indicating the lack of alternative enzymes capable of accomplishing this transferase reaction. Interestingly, PPT-silenced cells demonstrate significantly reduced proliferation and undergo strong G1 arrest, suggesting that the enzymatic function of PPT is essential and nonredundant. Our study identifies human PPT as the FDH-modifying enzyme and supports the hypothesis that mammals utilize a single enzyme for all phosphopantetheinylation reactions.
To prevent genetic code ambiguity due to misincorporation of amino acids into proteins, aminoacyl-tRNA synthetases have evolved editing activities to eliminate intermediate or final non-cognate products. In this work we studied the different editing pathways of class Ia leucyl-tRNA synthetase (LeuRS). Different mutations and experimental conditions were used to decipher the editing mechanism, including the recently developed compound AN2690 that targets the post-transfer editing site of LeuRS. The study emphasizes the crucial importance of tRNA for the pre- and post-transfer editing catalysis. Both reactions have comparable efficiencies in prokaryotic Aquifex aeolicus and Escherichia coli LeuRSs, although the E. coli enzyme favors post-transfer editing, whereas the A. aeolicus enzyme favors pre-transfer editing. Our results also indicate that the entry of the CCA-acceptor end of tRNA in the editing domain is strictly required for tRNA-dependent pre-transfer editing. Surprisingly, this editing reaction was resistant to AN2690, which inactivates the enzyme by forming a covalent adduct with tRNALeu in the post-transfer editing site. Taken together, these data suggest that the binding of tRNA in the post-transfer editing conformation confers to the enzyme the capacity for pre-transfer editing catalysis...
PR65 is the two-layered (α-α solenoid) HEAT-repeat (Huntingtin, elongation factor 3, a subunit of protein phosphatase 2A, PI3 kinase target of rapamycin 1) scaffold of protein phosphatase PP2A. Molecular dynamics simulations predict that, at forces expected in living systems, PR65 undergoes (visco-)elastic deformations in response to pulling/pushing on its ends. At lower forces, smooth global flexural and torsional changes occur via even redistribution of stress along the hydrophobic core of the molecule. At intermediate forces, helix–helix separation along one layer (“fracturing”) leads to global relaxation plus loss of contact in the other layer to unstack the affected units. Fracture sites are determined by unusual sequences in contiguous interhelix turns. Normal mode analysis of the heterotrimeric PP2A enzyme reveals that its ambient conformational fluctuations are dominated by elastic deformations of PR65, which introduce a mechanical linkage between the separately bound regulatory and catalytic subunits. PR65-dominated fluctuations of PP2A have the effect of opening and closing the enzyme’s substrate binding/catalysis interface, as well as altering the positions of certain catalytic residues. These results suggest that substrate binding/catalysis are sensitive to mechanical force. Force could be imposed from the outside (e.g....
Enzymes play a key role in almost all biological processes, accelerating a variety of metabolic reactions as well as controlling energy transduction, transcription and translation of genetic information, and signaling. They possess the remarkable capacity to accelerate reactions by many orders of magnitude compared to their uncatalyzed counterparts, making feasible crucial processes that would otherwise not occur on biologically relevant timescales. Thus, there is broad interest in understanding the catalytic power of enzymes on a molecular level. Several proposals have been put forward to try to explain this phenomenon, and one that has rapidly gained momentum in recent years is the idea that enzyme dynamics somehow contributes to catalysis. This review examines the dynamical proposal in a critical way considering basically all reasonable definitions, including (but not limited to) such proposed effects as “coupling between conformational and chemical motions”, “landscape searches” and “entropy funnels”. It is shown that none of these proposed effects have been experimentally demonstrated to contribute to catalysis, nor are they supported by consistent theoretical studies. On the other hand, it is clarified that careful simulation studies have excluded most (if not all) dynamical proposals. This review places significant emphasis on clarifying the role of logical definitions of different catalytic proposals...
The inositol monophosphatase (IMPase) enzyme from the hyperthermophilic archaeon Methanocaldococcus jannaschii requires Mg2+ for activity and binds three to four ions tightly in the absence of ligands: KD = 0.8 μM for one ion with a KD of 38 μM for the other Mg2+ ions. However, the enzyme requires 5–10 mM Mg2+ for optimum catalysis, suggesting substrate alters the metal ion affinity. In crystal structures of this archaeal IMPase with products, one of the three metal ions is coordinated by only one protein contact, Asp38. The importance of this and three other acidic residues in a mobile loop that approaches the active site was probed with mutational studies. Only D38A exhibited an increased kinetic KD for Mg2+; D26A, E39A, and E41A showed no significant change in the Mg2+ requirement for optimal activity. D38A also showed an increased Km, but little effect on kcat. This behavior is consistent with this side chain coordinating the third metal ion in the substrate complex, but with sufficient flexibility in the loop such that other acidic residues could position the Mg2+ in the active site in the absence of Asp38. While lithium ion inhibition of the archaeal IMPase is very poor (IC50∼250 mM), the D38A enzyme has a dramatically enhanced sensitivity to Li+ with an IC50 of 12 mM. These results constitute additional evidence for three metal ion assisted catalysis with substrate and product binding reducing affinity of the third necessary metal ion. They also suggest a specific mode of action for lithium inhibition in the IMPase superfamily.
The idea that tunneling is enhanced by the compression of the donor acceptor distance has attracted significant interest. In particular, recent studies argued that this proposal is consistent with pressure effects on enzymatic reactions, and that the observed pressure effects support the idea of vibrationally enhanced catalysis. However, a careful analysis of the current works reveals serious inconsistencies in the evidence presented to support these hypotheses. Apparently, tunneling decreases upon compression, and external pressure does not lead to the applicable compression of the free energy surface. Additionally, pressure experiments do not provide actual evidence for vibrationally enhanced catalysis. Finally, the temperature dependence of the entropy change in hydride transfer reactions is shown to reflect simple electrostatic effects.