Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases

The oxyanion hole of serine proteases is formed by the backbone N atoms of the catalytic Ser-195 and Gly-193 and engages the backbone O atom of the P1 residue of substrate in an important H-bonding interaction. The energetic contribution of this interaction in the ground and transition states is presently unknown. Measurements of the individual rate constants defining the catalytic mechanism of substrate hydrolysis for wild-type thrombin and trypsin and their G193A and G193P mutants reveal that Gly-193 is required for optimal substrate binding and acylation. Crystal structures of the G193A and G193P mutants of thrombin bound to the active site inhibitor H-d-Phe-Pro-Arg-CH2Cl document the extent of perturbation induced by the replacement of Gly-193. The Ala mutant weakens the H-bonding interaction of the N atom of residue 193, whereas the Pro substitution abrogates it altogether with additional small shifts of the protein backbone. From the kinetic and structural data, we estimate that the H-bonding interaction in the oxyanion hole contributes a stabilization of the ground and transition states of > 1.5 kcal/mol but < 3.0 kcal/mol. These results shed light on a basic aspect of the enzyme-substrate interaction in the entire family of trypsin-like serine proteases.     

Rigidification of the autolysis loop enhances Na(+) binding to thrombin

Binding of Na⁺ to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na⁺ is weak due to large heat capacity and enthalpy changes associated with binding, and the K_d = 80 mM ensures only 64% saturation of the site at the concentration of Na⁺ in the blood (140 mM). Residues controlling Na⁺ binding and activation have been identified. Yet, attempts to improve the interaction of Na⁺ with thrombin and possibly increase catalytic activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human thrombin with the homologous rigid domain of the murine enzyme results in a drastic (up to 10-fold) increase in Na⁺ affinity and a significant improvement in the catalytic activity of the enzyme. Rigidification of the autolysis loop abolishes the heat capacity change associated with Na⁺ binding observed in the wild-type and also increases the stability of thrombin. These findings have general relevance to protein engineering studies of clotting proteases and trypsin-like enzymes.     

Stabilization of the E* Form Turns Thrombin into an Anticoagulant

Previous studies have shown that deletion of nine residues in the autolysis loop of thrombin produces a mutant with an anticoagulant propensity of potential clinical relevance, but the molecular origin of the effect has remained unresolved. The x-ray crystal structure of this mutant solved in the free form at 1.55 Å resolution reveals an inactive conformation that is practically identical (root mean square deviation of 0.154 Å) to the recently identified E* form. The side chain of Trp²¹⁵ collapses into the active site by shifting >10 Å from its position in the active E form, and the oxyanion hole is disrupted by a flip of the Glu¹⁹²–Gly¹⁹³ peptide bond. This finding confirms the existence of the inactive form E* in essentially the same incarnation as first identified in the structure of the thrombin mutant D102N. In addition, it demonstrates that the anticoagulant profile often caused by a mutation of the thrombin scaffold finds its likely molecular origin in the stabilization of the inactive E* form that is selectively shifted to the active E form upon thrombomodulin and protein C binding.Serine proteases of the trypsin family are responsible for digestion, blood coagulation, fibrinolysis, development, fertilization, apoptosis, and immunity (1). Activation of the protease requires the transition from a zymogen form (2) and formation of an ion pair between the newly formed amino terminus of the catalytic chain and the side chain of the highly conserved residue Asp¹⁹⁴ (chymotrypsinogen numbering) next to the catalytic Ser¹⁹⁵. This ensures substrate access to the active site and proper formation of the oxyanion hole contributed by the backbone N atoms of Ser¹⁹⁵ and Gly¹⁹³ (3). The zymogen → protease conversion is classically associated with the onset of catalytic activity (3, 4) and provides a useful paradigm for understanding key features of protease function and regulation.Recent kinetic (5) and structural (6, 7) studies of thrombin, the key protease in the blood coagulation cascade (8), have drawn attention to a significant plasticity of the trypsin fold that impacts the function of the enzyme in a decisive manner. The active form of the protease, E, coexists with an inactive form, E*, that is distinct from the zymogen conformation (9). The E* form features a collapse of the 215–217 β-strand into the active site and a flip of the peptide bond between residues Glu¹⁹² and Gly¹⁹³ that disrupts the oxyanion hole. Importantly, the ion pair between Ile¹⁶ and Asp¹⁹⁴ remains intact, suggesting that E* is not equivalent to the zymogen form of the protease and that the E*-E equilibrium is established after the conversion from the zymogen form has taken place. Indeed, existing structures of the zymogen forms of trypsin (10), chymotrypsin (11), and chymase (12) feature a broken Ile¹⁶–Asp¹⁹⁴ ion pair but no collapse of the 215–217 β-strand. Stopped-flow experiments show that the E*-E conversion takes place on a time scale of <10 ms (5), as opposed to the much longer (100–1000 ms) time scale required for the zymogen-protease conversion (13, 14).The E* form is not a peculiarity of thrombin. The collapse of the 215–217 β-strand into the active site is observed in the inactive form of αI-tryptase (15), the high temperature requirement-like protease (16), complement factor D (17), granzyme K (18), hepatocyte growth factor activator (19), prostate kallikrein (20), and prostasin (21). A disrupted oxyanion hole is observed in complement factor B (22) and the arterivirus protease Nsp4 (23). The most likely explanation for the widespread occurrence of inactive conformations of trypsin-like proteases is that the E*-E equilibrium is a basic property of the trypsin fold that fine tunes activity and specificity once the zymogen → protease conversion has taken place (9).The new paradigm established by the E*-E equilibrium has obvious physiological relevance. In the case of complement factors, kallikreins, tryptase, and some coagulation factors must be kept to a minimum until binding of a trigger factor ensues. Stabilization of E* may afford a resting state of the protease waiting for action, as seen for other systems (24–28). For example, factor B is mostly inactive until binding of complement factor C3 unleashes catalytic activity at the site where amplification of C3 activation is most needed prior to formation of the membrane attack complex (29). Indeed, the crystal structure of factor B reveals a conformation with the oxyanion hole disrupted by a flip of the 192–193 peptide bond (22), as observed in the E* form of thrombin (6, 7).The allosteric equilibrium as shown in Scheme 1, involves the rates for the E* → E transition, k₁, and backward, k₋₁, that define the equilibrium constant r = k₋₁/k₁ = [E*]/[E] (5). The value of k_cat/K_m for an enzyme undergoing the E*-E equilibrium is as shown in Equation 1 (30), where s_E is the value of s for the E form, and obviously s_E* = 0. Likewise, the binding of an inhibitor to the enzyme undergoing the E*-E equilibrium is shown in Equation 2, where K_E is the value of the equilibrium association constant K for the E form, and K_E* = 0. As the value of r increases upon stabilization of E*, the values of s and K in Equations 1 and 2 decrease without limits. Hence, stabilization of E* has the potential to completely abrogate substrate hydrolysis (s → 0) or inhibitor binding (K → 0). However, binding of a suitable cofactor could restore activity by triggering the E* → E transition. This suggests a simple explanation for the anticoagulant profile observed in a number of thrombin mutants that have poor activity toward all physiological substrates but retain activity toward the anticoagulant protein C in the presence of the cofactor thrombomodulin (31–34). Here we report evidence that stabilization of E* provides a molecular mechanism to turn thrombin into an anticoagulant.     

Key residues controlling bidirectional ion movements in Na+/Ca2+ exchanger

Prokaryotic and eukaryotic Na⁺/Ca²⁺ exchangers (NCX) control Ca²⁺ homeostasis. NCX orthologs exhibit up to 10⁴-fold differences in their turnover rates (k_cat), whereas the ratios between the cytosolic (cyt) and extracellular (ext) K_m values (K_int = K_m^Cyt/K_m^Ext) are highly asymmetric and alike (K_int ≤ 0.1) among NCXs. The structural determinants controlling a huge divergence in k_cat at comparable K_int remain unclear, although 11 (out of 12) ion-coordinating residues are highly conserved among NCXs. The crystal structure of the archaeal NCX (NCX_Mj) was explored for testing the mutational effects of pore-allied and loop residues on k_cat and K_int. Among 55 tested residues, 26 mutations affect either k_cat or K_int, where two major groups can be distinguished. The first group of mutations (14 residues) affect k_cat rather than K_int. The majority of these residues (10 out of 14) are located within the extracellular vestibule near the pore center. The second group of mutations (12 residues) affect K_int rather than k_cat, whereas the majority of residues (9 out 12) are randomly dispersed within the extracellular vestibule. In conjunction with computational modeling-simulations and hydrogen-deuterium exchange mass-spectrometry (HDX-MS), the present mutational analysis highlights structural elements that differentially govern the intrinsic asymmetry and transport rates. The key residues, located at specific segments, can affect the characteristic features of local backbone dynamics and thus, the conformational flexibility of ion-transporting helices contributing to critical conformational transitions. The underlying mechanisms might have a physiological relevance for matching the response modes of NCX variants to cell-specific Ca²⁺ and Na⁺ signaling.     

Evidence that human α-thrombin is a monovalent cation-activated enzyme

The activity of human α-thrombin (EC 3.4.21.5) on small peptide substrates was enhanced by NaCl or KCl while tetramethylammonium chloride ((CH₃)₄NCl) or choline chloride (HO(CH₂)₂N(CH₃)₃Cl) which were used as ionic strength controls were without effect. The steady-state kinetic parameters of thrombin amidolysis of several peptidyl p-nitroanilide substrates were measured. Na⁺ enhanced thrombin activity by decreasing the K_m,app (0.2 to 0.7-fold) of all substrates, as well as increasing thombin turnover (3.4 to 4.5-fold) of some substrates. The average K_A for Na⁺for the four substrates examined was 3.5 × 10^?2m. A comparison of the effects of Na⁺ vs K⁺ on thrombin hydrolysis of a single substrate indicated that both cations similarly decreased the K_m,app (0.2 to 04.-fold) and increased thek_cat,app (3.1 to 3.4-fold) except that higher K⁺ concentrations (K_A = 2.8 × 10^?1M) were required. The rate of inactivation of thrombin by the active site-directed inhibitor N-p-tosyl-lysine chloromethyl ketone under pseudo-first-order conditions was enhanced 3-fold by saturating NaCl. Also, the fibrinogen clotting activity of thrombin was enhanced by NaCl compared to the choline chloride control. Spectral studies demonstrated that thrombin titration by Na⁺ caused a positive ultraviolet difference spectrum with maxima at 281.5 and 288.5 nm (Δ?_288.5 = +1067). The K_m for Na⁺ was 2.3 × 10^?2m which agrees with the kinetically determined K_A for Na⁺. The results are consistent with Na⁺ binding to thrombin causing a conformational change in the active site. It is concluded that human α-thrombin is a monovalent cation-activated enzyme.     

Sulphydryl groups of (Na+ + K+)-ATPase from rectal glands of Squalus acanthias: Detection of ligand-induced conformational changes

1. Modification of the Class II sulphydryl groups on the (Na⁺ + K⁺)-ATPase from rectal glands of Squalus acanthias with N-ethylmaleimide has been used to detect conformational changes in the protein. The rates of inactivation of the enzyme and the incorporation of N-ethylmaleimide depend on the ligands present in the incubation medium. With 150 mM K⁺ the rate of inactivation is largest (k₁ = 1.73 mM^?1 · min^?1) and four SH groups per α-subunit are modified. The rate of inactivation in the presence of 150 mM Na⁺ is smaller (k₁ = 1.08 mM^?1 · min^-1) but the incorporation of N-ethylmaleimide is the same as with K⁺. 2. ATP in micromolar concentrations protects the Class II groups in the presence of Na⁺ (k₁ = 0.08 mM^?1 · min^?1 at saturating ATP) and the incorporation id drastically reduced. ATP in millimolar concentrations protects the Class II groups partially in the presence of K⁺ (k₁ = 1.08 mM^?1 · min^?1) and three SH groups are labelled per α subunit. 3. The K⁺ -dependent phosphatase is inhibited in parallel to the (Na⁺ + K⁺)-ATPase under all conditions, and the ligand-dependent incorporation of N-ethylmaleimide was on the α-subunit only. 4. It is shown that the difference between the Na⁺ and K⁺ conformations sensed with N-ethylmaleimide depends on the pH of the incubation medium. At pH 6 there is a very small difference between the rates of inactivation in the presence of Na⁺ and K⁺, but at higher pH the difference increases. It is also shown that the rate of inactivation has a minimum at pH 6.9, which suggests that the conformation of the enzyme changes with pH. 5. Modification of the Class III groups with N-ethylmaleimide-whereby the enzyme activity is reduced from about 16% to zero-shows that these groups are also sensitive to conformational changes. As with the Class II groups, ATP in micromolar concentrations protects in the presence of Na⁺ relative to Na⁺ or K⁺ alone. ATP in millimolar concentrations with K⁺ present increases the rate of inactivation relative to K⁺ alone, in contrast to the effect on the Class II groups. 6. Modification of the Class II groups with a maleimide spin label shows a difference between Class II groups labelled in the presence of Na⁺ (or K⁺) and Class II groups labelled in the presence of K + ATP, in agreement with the difference in incorporation of N-ethylmaleimide. The spectra suggest that the SH group protected by ATP in the presence of K⁺ is buried in the protein. 7. The results suggest that at least four different conformations of the (Na⁺ + K⁺)-ATPase can be sensed with N-ethylmaleimide: (i) a Na⁺ form of the enzyme with ATP bound to a high-affinity site (E₁-Na-ATP); (ii) a Na⁺ form without ATP bound (E₁-Na); (iii) a K⁺ form without ATP bound (E₂-K); and (iv) an enzyme form with ATP bound to a low-affinity site in the presence of K⁺, probably and E₁-K-ATP form.     

Low Affinity and Slow Na+ Binding Precedes High Affinity Aspartate Binding in the Secondary-active Transporter GltPh

Glt_Ph from Pyrococcus horikoshii is a homotrimeric Na⁺-coupled aspartate transporter. It belongs to the widespread family of glutamate transporters, which also includes the mammalian excitatory amino acid transporters that take up the neurotransmitter glutamate. Each protomer in Glt_Ph consists of a trimerization domain involved in subunit interactions and a transport domain containing the substrate binding site. Here, we have studied the dynamics of Na⁺ and aspartate binding to Glt_Ph. Tryptophan fluorescence measurements on the fully active single tryptophan mutant F273W revealed that Na⁺ binds with low affinity to the apoprotein (K_d 120 mm), with a particularly low k_on value (5.1 m⁻¹s⁻¹). At least two sodium ions bind before aspartate. The binding of Na⁺ requires a very high activation energy (E_a 106.8 kJ mol⁻¹) and consequently has a large Q₁₀ value of 4.5, indicative of substantial conformational changes before or after the initial binding event. The apparent affinity for aspartate binding depended on the Na⁺ concentration present. Binding of aspartate was not observed in the absence of Na⁺, whereas in the presence of high Na⁺ concentrations (above the K_d for Na⁺) the dissociation constants for aspartate were in the nanomolar range, and the aspartate binding was fast (k_on of 1.4 × 10⁵ m⁻¹s⁻¹), with low E_a and Q₁₀ values (42.6 kJ mol⁻¹ and 1.8, respectively). We conclude that Na⁺ binding is most likely the rate-limiting step for substrate binding.     

Nickel(II) ion-catalyzed hydrolysis of acetyl esters of 2-pyridineoxime derivatives: Effects of geometry around central metal atom on the efficiency of metal ion catalysis

The kinetics of the Ni(II)-catalyzed ester hydrolysis of O-acetyl-2-pyridine-carboxaldoxime, O-acetyl-2-acetylpyridineketoxime, and O-acetyl-6-carboxy-2-pyridine-carboxaldoxime are measured and the values of various k_cat parameters are calculated for reaction paths involving one metal ion (k_cat^W and k_cat^OH) and two metal ions k_cat^A and k_cat^B). Examination of the kinetic data reveals that the k_cat^W and k_cat^OH paths for the Ni(II)-catalyzed reactions involve the same mechanism as those for the previously reported Cu(II)-catalyzed reactions. For the k_cat^A and k_cat^B paths, the mechanism involving binuclear Ni(II) ions is preferred by analogy with the previously reported Zn(II)-catalyzed reactions. Comparison of k_cat^OH values for the Cu(II)- and Ni(II)-catalyzed hydrolysis of 1–3 indicates that markedly different steric effects are exerted by the substituents of 2 and 3 on the catalytic behavior of the two metal ions. This is explained in terms of differences in the fit of the metal ions in the metal complexes of 1–3. Present results demonstrate that slight changes in the geometry around the central metal atom can affect the catalytic outcome significantly. The implications of the present results on metal substitution in metalloenzymes are also discussed.     

In rat dipeptidyl peptidase III,His is essential for catalysis,and Glu or Glu stabilizes the coordination bond between His or His and zinc ion

Dipeptidyl peptidase (DPP) III is a zinc-dependent exopeptidase that has a unique motif, “HELLGH,” as the zinc-binding site. In the present study, a three-dimensional (3D) model of rat DPP III was generated with the X-ray crystal structure of human DPP III (PDB: 3FVY [Dobrovetsky E. et al. (2009) SGC]) as a template. The replacement of the seven charged amino acid residues with a hydrophobic amino acid around the zinc ion did not cause any significant changes in K_m values or in the substrate specificity. However, the k_cat values of H568R and H568Y were remarkably reduced, by factors of 50 and 400, respectively. The His⁵⁶⁸ residue of rat DPP III is essential for enzyme catalysis. The k_cat values of the mutants E507A and E512A were 2.38 and 3.88 s^− 1 toward Arg-Arg-NA, and 0.097 and 0.59 s⁻¹ toward Phe-Arg-NA, respectively. These values were markedly lower than those of the wild-type DPP III. Furthermore, the zinc contents of E507A and E512A were 0.29 and 0.08 atom per mol of protein, respectively, and those mutations caused remarkable increases in the dissociation constants of the zinc ions from DPP III by factors of 5 × 10³ to 2 × 10⁴. The 3D model of the catalytic domain of rat DPP III showed that the carboxyl oxygen atoms of Glu⁵⁰⁷ and Glu⁵¹² form the hydrogen bonds to the nitrogen atoms of His⁴⁵⁵ and His⁴⁵⁰. All of these results showed that Glu⁵⁰⁷ or Glu⁵¹² stabilizes the coordination bond between the zinc ion and His⁴⁵⁵ or His⁴⁵⁰.     

Engineering protein allostery: 1.05 A resolution structure and enzymatic properties of a Na+-activated trypsin

Some trypsin-like proteases are endowed with Na⁺-dependent allosteric enhancement of catalytic activity, but this important mechanism has been difficult to engineer in other members of the family. Replacement of 19 amino acids in Streptomyces griseus trypsin targeting the active site and the Na⁺-binding site were found necessary to generate efficient Na⁺ activation. Remarkably, this property was linked to the acquisition of a new substrate selectivity profile similar to that of factor Xa, a Na⁺-activated protease involved in blood coagulation. The X-ray crystal structure of the mutant trypsin solved to 1.05 Å resolution defines the engineered Na⁺ site and active site loops in unprecedented detail. The results demonstrate that trypsin can be engineered into an efficient allosteric protease, and that Na⁺ activation is interwoven with substrate selectivity in the trypsin scaffold.     

Mechanism of action of thrombin on fibrinogen. Reaction of the N-terminal CNBr fragment from the Aalpha chain of human fibrinogen with bovine thrombin

The 51-residue N-terminal cyanogen bromide fragment from the Aα chain of human fibrinogen was isolated, and the Michaelis-Menten constants, K_m and k_cat, for its hydrolysis by bovine thrombin were determined. The measured values of K_m and k_cat are 4.7 × 10^?5m and 4.8 × 10^?10m [(NIH U/liter) sec]^?1, respectively. Since these values are similar to those for fibrinogen, it appears that the N-terminal CNBr fragment contains all amino acid residues whose interactions with thrombin account for the high specificity of this enzyme for fibrinogen.     

Conserved water molecules in the specificity pocket of serine proteases and the molecular mechanism of Na+ binding

Conservation of clusters of buried water molecules is a structural motif present throughout the serine protease family. Frequently, these clusters are shaped as water channels forming extensive hydrogen-bonding networks linked to the protein backbone. The most conspicuous example is the water channel present in the specificity pocket of trypsin and thrombin. In thrombin, other vitamin K-dependent proteases, and some complement factors, Na⁺ binds in this water channel and enhances allosterically the catalytic activity of the enzyme, whereas digestive and fibrinolytic proteases are devoid of such regulation. A comparative analysis of proteases with and without Na⁺ binding capability reveals the role of the water channel in maintaining the structural organization of the specificity pocket and in Na⁺ coordination. This enables the formulation of a molecular mechanism for Na⁺ binding in thrombin and leads to the identification of the structural changes necessary to engineer a functional Na⁺ site and enhanced catalytic activity in trypsin and other proteases. Proteins 30:34–42, 1998. © 1998 Wiley-Liss, Inc.     

Thrombin Specificity: Further Evidence for the Importance of the β-Insertion Loop and Trp96. Implications of the Hydrophobic Interaction Between Trp96 and Pro60B Pro60C for the Activity of Thrombin

A number of thrombin mutants have been constructed to investigate the role of Trp⁹⁶ and the β-insertion loop for the specificity of thrombin. Thrombin(60D) consists of the replacement of the β-insertion loop (14 amino acid residues from 59 to 63, including a 9-residue insertion at position 60) with the corresponding four residues in trypsin, Tyr-Lys-Ser-Gly; thrombin(GGG) is a smaller loop mutation in which the residues Tyr^60APro^60BPro^60CTrp^60D Asp^60ELys^60F of the β-insertion loop were replaced by Gly-Gly-Gly; thrombin(96S) consists of a point mutation Trp⁹⁶→Ser; and thrombin(GGG/96S) is the double mutant incorporating both changes. Thrombin(96S) clots fibrinogen ~3 times more slowly than thrombin, with the two β-insertion loop mutants, thrombin(GGG) and thrombin(GGG/96S), reacting ~3000- and 1300-fold more slowly, respectively. The specificity constant k _cat/K _m for the cleavage of fibrinopeptide A and fibrinopeptide B by thrombin(96S) was 2.6 and 0.35 μM^?1 s^?1 respectively, compared to 10 and 2.5 μM^?1 s^?1 for wild-type recombinant thrombin, respectively. Kinetic constants were determined for the hydrolysis of H-D-phenylalanyl-L-pipecolyl-L-arginine-p-nitroaniline. The Michaelis constant K _m increased ~6-fold for thrombin(96S) and >200-fold for thrombin(GGG) and thrombin(GGG/96S) when compared to wild-type recombinant thrombin, while the catalytic constant k _cat remained approximately the same. All mutants were more susceptible to inhibition by BPTI than wild-type recombinant thrombin. Clearly, the β-insertion loop is important for thrombin activity. But the mutation of Trp⁹⁶→Ser can compensate somewhat for the loss of binding at the β-insertion loop. The deletion of the hydrophobic interaction between Trp⁹⁶ and Pro^60BPro^60C appears to decrease the stability of the β-insertion loop, thereby causing a decrease in binding efficiency.     

The base exchange reaction of NAD+ glycohydrolase: identification of novel heterocyclic alternative substrates

ADP-ribosyl cyclase and NAD⁺ glycohydrolase (CD38, E.C.3.2.2.5) efficiently catalyze the exchange of the nicotinamidyl moiety of NAD⁺, nicotinamide adenine dinucleotide phosphate (NADP⁺) or nicotinamide mononucleotide (NMN⁺) with an alternative base. 4′-Pyridinyl drugs (amrinone, milrinone, dismerinone and pinacidil) were efficient alternative substrates (k_cat/K_M = 0.9-10 μM⁻¹ s⁻¹) in the exchange reaction with ADP-ribosyl cyclase. When CD38 was used as a catalyst the k_cat/K_M values for the exchange reaction were reduced two or more orders of magnitude (0.015-0.15 μM⁻¹ s⁻¹). The products of this reaction were novel dinucleotides. The values of the equilibrium constants for dinucleotide formation were determined for several drugs. These enzymes also efficiently catalyze the formation of novel mononucleotides in an exchange reaction with NMN⁺, k_cat/K_M = 0.05-0.4 μM⁻¹ s⁻¹. The k_cat/K_M values for the exchange reaction with NMN⁺ were generally similar (0.04-0.12 μM⁻¹ s⁻¹) with CD38 and ADP-ribosyl cyclase as catalysts. Several novel heterocyclic alternative substrates were identified as 2-isoquinolines, 1,6-naphthyridines and tricyclic bases. The k_cat/K_M values for the exchange reaction with these substrates varied over five orders of magnitude and approached the limit of diffusion with 1,6-naphthyridines. The exchange reaction could be used to synthesize novel mononucleotides or to identify novel reversible inhibitors of CD38.     

N 6-Methyladenosines in mRNAs reduce the accuracy of codon reading by transfer RNAs and peptide release factors

We used quench flow to study how N⁶-methylated adenosines (m⁶A) affect the accuracy ratio between k_cat/K_m (i.e. association rate constant (k_a) times probability (P_p) of product formation after enzyme-substrate complex formation) for cognate and near-cognate substrate for mRNA reading by tRNAs and peptide release factors 1 and 2 (RFs) during translation with purified Escherichia coli components. We estimated k_cat/K_m for Glu-tRNA^Glu, EF-Tu and GTP forming ternary complex (T₃) reading cognate (GAA and Gm⁶AA) or near-cognate (GAU and Gm⁶AU) codons. k_a decreased 10-fold by m⁶A introduction in cognate and near-cognate cases alike, while P_p for peptidyl transfer remained unaltered in cognate but increased 10-fold in near-cognate case leading to 10-fold amino acid substitution error increase. We estimated k_cat/K_m for ester bond hydrolysis of P-site bound peptidyl-tRNA by RF2 reading cognate (UAA and Um⁶AA) and near-cognate (UAG and Um⁶AG) stop codons to decrease 6-fold or 3-fold by m⁶A introduction, respectively. This 6-fold effect on UAA reading was also observed in a single-molecule termination assay. Thus, m⁶A reduces both sense and stop codon reading accuracy by decreasing cognate significantly more than near-cognate k_cat/K_m, in contrast to most error inducing agents and mutations, which increase near-cognate at unaltered cognate k_cat/K_m.     

Functional and Structural Characterization of Vibrio cholerae Extracellular Serine Protease B,VesB

The chymotrypsin subfamily A of serine proteases consists primarily of eukaryotic proteases, including only a few proteases of bacterial origin. VesB, a newly identified serine protease that is secreted by the type II secretion system in Vibrio cholerae, belongs to this subfamily. VesB is likely produced as a zymogen because sequence alignment with trypsinogen identified a putative cleavage site for activation and a catalytic triad, His-Asp-Ser. Using synthetic peptides, VesB efficiently cleaved a trypsin substrate, but not chymotrypsin and elastase substrates. The reversible serine protease inhibitor, benzamidine, inhibited VesB and served as an immobilized ligand for VesB affinity purification, further indicating its relationship with trypsin-like enzymes. Consistent with this family of serine proteases, N-terminal sequencing implied that the propeptide is removed in the secreted form of VesB. Separate mutagenesis of the activation site and catalytic serine rendered VesB inactive, confirming the importance of these features for activity, but not for secretion. Similar to trypsin but, in contrast to thrombin and other coagulation factors, Na⁺ did not stimulate the activity of VesB, despite containing the Tyr²⁵⁰ signature. The crystal structure of catalytically inactive pro-VesB revealed that the protease domain is structurally similar to trypsinogen. The C-terminal domain of VesB was found to adopt an immunoglobulin (Ig)-fold that is structurally homologous to Ig-folds of other extracellular Vibrio proteins. Possible roles of the Ig-fold domain in stability, substrate specificity, cell surface association, and type II secretion of VesB, the first bacterial multidomain trypsin-like protease with known structure, are discussed.     

Identification of a Xylitol Dehydrogenase Gene from Kluyveromyces marxianus NBRC1777

Xylitol dehydrogenase (XDH) (EC 1.1.1.9) is one of the key enzymes in the xylose fermentation pathway in yeast and fungi. A xylitol dehydrogenase gene (XYL2) encoding a XDH was cloned from Kluyveromyces marxianus NBRC 1777, and the in vivo function was validated by disruption and complementation analysis. The highest activity of KmXDH could be observed at pH 9.5 during 55°C. The values of k _cat/K _m indicate that KmXDH prefers NAD⁺ to NADP⁺ (k _cat/K _{m NAD} ⁺ 3681/min mM and k _cat/K _{m NADP} ⁺ 1361/min mM). The different coenzyme preference between KmXR and KmXDH caused an accumulation of NADH in the xylose utilization pathway. The redox imbalance may be one of the reasons to cause the poor xylose fermentation under oxygen-limited conditions in K. marxianus NBRC1777.     

The Rapid-onset Dystonia Parkinsonism Mutation D923N of the Na+,K+-ATPase α3 Isoform Disrupts Na+ Interaction at the Third Na+ Site

Rapid-onset dystonia parkinsonism (RDP), a rare neurological disorder, is caused by mutation of the neuron-specific α3-isoform of Na⁺,K⁺-ATPase. Here, we present the functional consequences of RDP mutation D923N. Relative to the wild type, the mutant exhibits a remarkable ∼200-fold reduction of Na⁺ affinity for activation of phosphorylation from ATP, reflecting a defective interaction of the E₁ form with intracellular Na⁺. This is the largest effect on Na⁺ affinity reported so far for any Na⁺,K⁺-ATPase mutant. D923N also affects the interaction with extracellular Na⁺ normally driving the E₁P to E₂P conformational transition backward. However, no impairment of K⁺ binding was observed for D923N, leading to the conclusion that Asp⁹²³ is specifically associated with the third Na⁺ site that is selective toward Na⁺. The crystal structure of the Na⁺,K⁺-ATPase in E₂ form shows that Asp⁹²³ is located in the cytoplasmic half of transmembrane helix M8 inside a putative transport channel, which is lined by residues from the transmembrane helices M5, M7, M8, and M10 and capped by the C terminus, recently found involved in recognition of the third Na⁺ ion. Structural modeling of the E₁ form of Na⁺,K⁺-ATPase based on the Ca²⁺-ATPase crystal structure is consistent with the hypothesis that Asp⁹²³ contributes to a site binding the third Na⁺ ion. These results in conjunction with our previous findings with other RDP mutants suggest that a selective defect in the handling of Na⁺ may be a general feature of the RDP disorder.     

Intracellular Na+ Regulates Epithelial Na+ Channel Maturation

Epithelial Na⁺ channel (ENaC) function is regulated by the intracellular Na⁺ concentration ([Na⁺]_i) through a process known as Na⁺ feedback inhibition. Although this process is known to decrease the expression of proteolytically processed active channels on the cell surface, it is unknown how [Na⁺]_i alters ENaC cleavage. We show here that [Na⁺]_i regulates the posttranslational processing of ENaC subunits during channel biogenesis. At times when [Na⁺]_i is low, ENaC subunits develop mature N-glycans and are processed by proteases. Conversely, glycan maturation and sensitivity to proteolysis are reduced when [Na⁺]_i is relatively high. Surface channels with immature N-glycans were not processed by endogenous channel activating proteases, nor were they sensitive to cleavage by exogenous trypsin. Biotin chase experiments revealed that the immature surface channels were not converted into mature cleaved channels following a reduction in [Na⁺]_i. The hypothesis that [Na⁺]_i regulates ENaC maturation within the biosynthetic pathways is further supported by the finding that Brefeldin A prevented the accumulation of processed surface channels following a reduction in [Na⁺]_i. Therefore, increased [Na⁺]_i interferes with ENaC N-glycan maturation and prevents the channel from entering a state that allows proteolytic processing.     

Novel internally quenched substrate of the trypsin-like subunit of 20S eukaryotic proteasome

This article describes the synthesis, using combinatorial chemistry, of internally quenched substrates of the trypsin-like subunit of human 20S proteasome. Such substrates were optimized in both the nonprime and prime regions of the peptide chain. Two were selected as the most susceptible for proteasomal proteolysis with excellent kinetic parameters: (i) ABZ-Val-Val-Ser-Arg-Ser-Leu-Gly-Tyr(3-NO₂)-NH₂ (k_cat/K_M = 934,000 M⁻¹ s⁻¹) and (ii) ABZ-Val-Val-Ser-GNF-Ala-Met-Gly-Tyr(3-NO₂)-NH₂ (k_cat/K_M = 1,980,000 M⁻¹ s⁻¹). Both compounds were efficiently hydrolyzed by the 20S proteasome at picomolar concentrations, demonstrating significant selectivity over other proteasome entities.