Coenzyme-binding Domain Research Articles

Effects of NAD+ binding on the luminescence of tryptophans 84 and 310 of glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus.

The individual fluorescence and phosphorescence properties of W84 and W310 in Bacillus stearothermophilus glyceraldehyde-3-phosphate dehydrogenase were identified through the construction of a single tryptophan mutant (W84F) and by comparison of the emission between mutant and wild-type enzymes. The results show that the luminescence of W310 is red-shifted and substantially quenched relative to that of W84. It displays an average subnanosecond fluorescence lifetime (tau F) and a very short, 50 microseconds, room-temperature phosphorescence (RTP) lifetime (tau P). The perturbation of W310 luminescence is believed to arise from a stacking interaction with Y283. In contrast, W84 exhibits a fluorescence lifetime tau F of several nanoseconds and a long-lived phosphorescence lifetime tau P, typical of buried, unperturbed TrP residues. NAD+ binding to the tetrameric enzyme causes a 55% reduction of W310 fluorescence intensity together with a nearly complete quenching of its low-temperature phosphorescence. W84, which is located far from the nicotinamide moiety of NAD+, is much less affected by the binding of the coenzyme; the reduction in fluorescence intensity is 35%, and its phosphorescence intensity is unchanged. Another consequence of NAD+ binding is a significant decrease of the RTP lifetime tau P of W84, manifesting thereby a conformational change in the region of the coenzyme-binding domain. However, no change is observed in the RTP lifetime tau P of W310 located in the catalytic domain. These findings and those obtained at partial coenzyme saturation support the conclusions derived from high-resolution crystallographic structures [Skarzynski, T., & Wonacott, A. J., (1988) J. Mol. Biol. 203, 1097-1118] that the NAD(+)-induced conformational change is sequential and that subtle rearrangement in the structure of unligated subunits might be responsible for the negative cooperative behavior of NAD+ binding.

Circular permutation within the coenzyme binding domain of the tetrameric glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus.

A circularly permuted (cp) variant of the phosphorylating NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus stearothermophilus has been constructed with N- and C-termini created within the coenzyme binding domain. The cp variant has a kcat value equal to 40% of the wild-type value, whereas Km and KD values for NAD show a threefold decrease compared to wild type. These results indicate that the folding process and the conformational changes that accompany NAD binding during the catalytic event occur efficiently in the permuted variant and that NAD binding is tighter. Reversible denaturation experiments show that the stability of the variant is only reduced by 0.7 kcal/mol compared to the wild-type enzyme. These experiments confirm and extend results obtained recently on other permuted proteins. For multimeric proteins, such as GAPDH, which harbor subunits with two structural domains, the natural location of the N- and C-termini is not a prerequisite for optimal folding and biological activity.

Structure of 6-phosphogluconate dehydrogenase refined at 2 A resolution.

The X-ray unliganded structure of 6-phosphogluconate dehydrogenase (E.C. 1.1.1.44) (6-PGDH) from sheep liver has been determined at 2A resolution and refined to a final R-factor of 19.8% for 35 031 unique reflections. The enzyme is dimeric, each subunit being comprised of an N-terminal coenzyme-binding domain with a Rossmann fold, a large all-helical domain and a small C-terminal tail. The model contains 473 residues, three sulfate ions and 346 water molecules; the two best defined sulfates are found in the active site. This structure, based on improved diffraction data, is an extension of the 2.5 A, resolution model reported earlier. It has good geometry with 92% of the residues falling in the most favoured areas of the Ramachandran plot. Several unusual features are discussed: the incorporation of an alanine in place of the second conserved glycine of the dinucleotide-binding fingerprint; a duplicated five-helix motif which is unique to this enzyme; an extended water network at the dimer interface and a C-terminal tail which is incorporated within the second subunit, forming not only a major part of the dimer interface but also part of the active site.

Short-chain dehydrogenases/reductases.

The family of short-chain dehydrogenases/reductases (SDR) with subunits of typically 250-odd amino acid residues now encompasses 57 different characterised proteins, representing a wide variety of enzyme activities. The first characterised member of this family was the fruit-fly alcohol dehydrogenase (Schwartz and Jörnvall, 1976; Thatcher, 1980). This alcohol dehydrogenase is different from the classical liver alcohol dehydrogenase, which has larger subunits of about 370 residues, is zinc-dependent, and belongs to a family of medium-chain dehydrogenases/reductases (MDR) (Jörnvall et al., 1981; Persson et al., 1994). In the early 80’s, two additional structures were shown to be related to the Drosophila alcohol dehydrogenase (Jörnvall et al., 1981, 1984), thus establishing a new enzyme family. These structures were glucose dehydrogenase (Jany et al., 1984) and ribitol dehydrogenase (Morris et al., 1974; Dothie et al., 1985). Already at this stage, it was seen that the molecular architecture was different between this short-chain dehydrogenase family and the medium-chain dehydrogenases. The coenzyme-binding region is located at the beginning of the C-terminal domain in the medium-chain dehydrogenases, with a classical Rossmann fold (Rossmann et al., 1975) and a conserved Gly-X-Gly-X-X-Gly pattern. In contrast, the short-chain dehydrogenases have a similar pattern of Gly-X-Gly-X-X-X-Gly at the N-terminal region. In addition, secondary structure predictions suggested this region to have a β-turn-α-turn-β motif, compatible with a Rossmann fold (Thatcher & Sawyer, 1980). Consequently, it was early clear that the two different families of dehydrogenases have different molecular architectures. The medium-chain dehydrogenases have an N-terminal, catalytic domain and a C-terminal, coenzyme-binding domain, while in the shortchain dehydrogenases the coenzyme-binding is located N-terminally and the catalytic site toward the C-terminal half of the molecule (Jörnvall et al., 1981).

Mechanism of inhibition of carbonyl reductase from rabbit kidney by phenylbutazone.

Phenylbutazone showed significant inhibition against the metabolic reduction of acetohexamide catalyzed by carbonyl reductase purified from rabbit kidney. Thus, the inhibitory effect of phenylbutazone was kinetically examined. Phenylbutazone was a competitive inhibitor for the enzyme with respect to NADPH, whereas it noncompetitively inhibited the enzyme activity with respect to acetohexamide. A fluorescence study revealed that phenylbutazone decreases the binding of NADPH to the free enzyme (apoenzyme). These results suggest that phenylbutazone causes the inhibition of carbonyl reductase by competing with NADPH in its coenzyme-binding domain.

The three-dimensional structure of glucose 6-phosphate dehydrogenase from Leuconostoc mesenteroides refined at 2.0 A resolution.

Glucose 6-phosphate dehydrogenase (G6PD) is the first enzyme of the pentose phosphate pathway. Normally the pathway is synthetic and NADP-dependent, but the Gram-positive bacterium Leuconostoc mesenteroides, which does not have a complete glycolytic pathway, also uses the oxidative enzymes of the pentose phosphate pathway for catabolic reactions, and selects either NAD or NADP depending on the demands for catabolic or anabolic metabolism. The structure of G6PD has been determined and refined to 2.0 A resolution. The enzyme is a dimer, each subunit consisting of two domains. The smaller domain is a classic dinucleotide-binding fold, while the larger one is a new beta+ alpha fold, not previously seen, with a predominantly antiparallel nine-stranded beta-sheet. There are significant structural differences in the coenzyme-binding domains of the two subunits, caused by Pro 149 which is cis in one subunit and trans in the other. The structure has allowed us to propose the location of the active site and the coenzyme-binding site, and suggests the role of many of the residues conserved between species. We propose that the conserved Arg46 would interact with both the adenine ring and the 2'-phosphate of NADP. Gln47, which is not conserved, may contribute to the change from NADP to dual coenzyme specificity. His178, in a nine-residue peptide conserved for all known sequences, binds a phosphate in the active site pocket. His240 is the most likely candidate for the base to oxidize the 1-hydroxyl group of the glucose 6-phosphate substrate.

Fundamental molecular differences between alcohol dehydrogenase classes.

Two types of alcohol dehydrogenase in separate protein families are the "medium-chain" zinc enzymes (including the classical liver and yeast forms) and the "short-chain" enzymes (including the insect form). Although the medium-chain family has been characterized in prokaryotes and many eukaryotes (fungi, plants, cephalopods, and vertebrates), insects have seemed to possess only the short-chain enzyme. We have now also characterized a medium-chain alcohol dehydrogenase in Drosophila. The enzyme is identical to insect octanol dehydrogenase. It is a typical class III alcohol dehydrogenase, similar to the corresponding human form (70% residue identity), with mostly the same residues involved in substrate and coenzyme interactions. Changes that do occur are conservative, but Phe-51 is of functional interest in relation to decreased coenzyme binding and increased overall activity. Extra residues versus the human enzyme near position 250 affect the coenzyme-binding domain. Enzymatic properties are similar--i.e., very low activity toward ethanol (Km beyond measurement) and high selectivity for formaldehyde/glutathione (S-hydroxymethylglutathione; kcat/Km = 160,000 min-1.mM-1). Between the present class III and the ethanol-active class I enzymes, however, patterns of variability differ greatly, highlighting fundamentally separate molecular properties of these two alcohol dehydrogenases, with class III resembling enzymes in general and class I showing high variation. The gene coding for the Drosophila class III enzyme produces an mRNA of about 1.36 kb that is present at all developmental stages of the fly, compatible with the constitutive nature of the vertebrate enzyme. Taken together, the results bridge a previously apparent gap in the distribution of medium-chain alcohol dehydrogenases and establish a strictly conserved class III enzyme, consistent with an important role for this enzyme in cellular metabolism.

Conformational changes in proteins induced by dynamic associations. A tryptophan phosphorescence study

Random collisions between macromolecules lead to dynamic associations (lengthy encounters) that in principle could affect their conformation and, in the case of enzymes, their binding and catalytic properties. Exploiting the unique sensitivity of the phosphorescence lifetime, tau, of Trp to the internal flexibility of globular proteins we probed the perturbations induced in the structure of the coenzyme-binding domain of alcohol dehydrogenase (LADH) and glyceraldehyde-3-phosphate dehydrogenase (GraPDH) by the presence in solution of other dehydrogenases and of functionally unrelated proteins. With Trp314 of LADH, the results emphasize that while tau is not affected by the concentration of LADH itself, the addition of micromolar quantities of other proteins causes a distinct reduction in it. From the linear increase of 1/tau with protein concentration one obtains values for the apparent second-order Stern-Volmer rate constant that range between 2-200 x 10(3) M-1 s-1, decreasing 2-3-fold when ternary complexes of LADH with NADH or NAD+ and inhibitors are involved. Similar effects were observed with Trp310 of GraPDH except that with sorbitol dehydrogenase as perturbant the increase of 1/tau is hyperbolic and governed by an apparent dissociation constant of about 1 microM. Finally, glycerol-3-phosphate dehydrogenase, the strongest perturber of both LADH and GraPDH, has either no effect on lactic dehydrogenase from pig heart or induces a moderate lengthening of the triplet lifetime of the rabbit muscle enzyme. Because Stern-Volmer behavior is typical also of diffusion-mediated quenching reactions, a parallel investigation with cysteine, cystine and N-acetyl-tryptophanamide demonstrated that among potential, protein-associated, quenching moieties namely, -SH, -S-S- and indole groups, only the latter has rate constants approaching the magnitude of protein perturbants. Since considerable evidence rules out the predominance of such quenching reactions, these findings confirm a subtle form of communication between protein molecules in solution. The lack of specificity and the similar effects between dehydrogenases with right and wrong stereospecificity for direct coenzyme transfer suggests that the perturbations monitored are unrelated to this function.

Autonomous folding of the excised coenzyme‐binding domain of D‐glyceraldehyde 3‐phosphate dehydrogenase from Thermotoga maritima

An important question in protein folding is whether compact substructures or domains are autonomous units of folding and assembly. The protomer of the tetrameric D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima has a complex coenzyme-binding domain, in which residues 1-146 form a compact substructure with the last 31 residues (313-333). Here it is shown that the gene of a single-chain protein can be expressed in Escherichia coli after deleting the 163 codons corresponding to the interspersed catalytic domain (150-312). The purified gene product is a soluble, monomeric protein that binds both NAD+ and NADH strongly and possesses the same unfolding transition induced by guanidinium chloride as the native tetramer. The autonomous folding of the coenzyme-binding domain has interesting implications for the folding, assembly, function, and evolution of the native enzyme.

High Resolution Structures of Holo and Apo Formate Dehydrogenase

Three-dimensional crystal structures of holo (ternary complex enzyme-NAD-azide) and apo NAD-dependent dimeric formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 have been refined to R factors of 11·7% and 14·8% at 2·05 and 1·80 Å resolution, respectively. The estimated root-mean-square error in atomic co-ordinates is 0·11 Å for holo and 0·18 Å for apo. X-ray data were collected from single crystals using an imaging plate scanner and synchrotron radiation. In both crystal forms there is a dimer in the asymmetric unit. Both structures show essentially 2-fold molecular symmetry. NAD binding causes movement of the catalytic domain and ordering of the C terminus, where a new helix appears. This completes formation of the enzyme active centre in holo FDH. NAD is bound in the cleft separating the domains and mainly interacts with residues from the co-enzyme binding domain. In apo FDH these residues are held in essentially the same conformation by water molecules occupying the NAD binding region. An azide molecules is located the point of catalysis, the C4 atom of the nicotinamide moiety of NAD, and overlaps with the proposed formate binding. There is an extensive channel running from the active site to the protein surface and this is supposed to be used by substrate to reach the active centre after NAD has already bound. The structure of the active site and a hypothetical catalytic mechanism are discussed. Sequence homology of FDH with other NAD-dependent formate dehydrogenases and some d -specific dehydrogenases is discussed on the basis of the FDH three-dimensional structure.

The crystal structure of the aldose reductase.NADPH binary complex.

Aldose reductase is an NADPH-dependent oxidoreductase that catalyzes the reduction of a broad range of aldehydes, including glucose. Since aldose reductase has been strongly implicated in the development of the chronic complications of diabetes mellitus, much effort has been devoted to understanding the structure and mechanism of this enzyme, and many aldose reductase inhibitors have been developed as potential drugs for the treatment of these complications. We describe here the 2.75 A crystal structure of recombinant human aldose reductase (Cys-298 to Ser mutant) complexed with NADPH. This mutant displays unusual kinetic behavior characterized by high Km/high Vmax substrate kinetics and reduced sensitivity to certain aldose reductase inhibitors. The crystal structure revealed that the enzyme is a beta/alpha-barrel with the coenzyme-binding domain located at the carboxyl-terminal end of the parallel strands of the barrel. The enzyme undergoes a large conformational change upon binding NADPH which involves the reorientation of loop 7 to a position which appears to lock the coenzyme into place. NADPH is bound to aldose reductase in an unusual manner, more similar to FAD- rather than NAD(P)-dependent oxidoreductases. No disulfide bridges were observed in the crystal structure.

Chemical modification of arginine and lysine residues in coenzyme-binding domain of carbonyl reductase from rabbit kidney: indomethacin affords a significant protection against inactivation of the enzyme by phenylglyoxal

Carbonyl reductase from rabbit kidney was inactivated by phenylglyoxal (PGO) and 2,4,6-trinitrobenzenesulfonate sodium (TNBS). NADP + protected the enzyme from the inactivations by PGO and TNBS, suggesting that essential arginine and lysine residues are located in coenzyme-binding domain of the enzyme. Judging from the effects of PGO-treated enzymes in the presence and in the absence of NADP + on the fluorescence intensity of NADPH, one essential arginine residue in coenzyme-binding domain was found to have a role in the binding of NADPH to the enzyme. Indomethacin afforded a significant protection against inactivation of the enzyme by PGO, whereas it could not protect the enzyme from the inactivation by TNBS. It is reasonable to postulate that indomethacin interacts at least in part with or near one essential arginine residue in coenzyme-binding domain of carbonyl reductase from rabbit kidney.

Chemical modification of octopine dehydrogenase by thiol-specific reagents: evidence for the presence of an essential cysteine at the catalytic site

Thiol-specific reagents, p-cchloromercuricphenyl sulfonic acid (PCMS), 5,5′-dithiobis-(2-nitrobenzoic acid) (DTNB) and N-ethylmaleimide (NEM), incubated with octopine dehydrogenase resulted in the loss of catalytic activity. The kinetic profile of PCMS inactivated enzyme showed that the reaction followed pseudo-first-order kinetics during the initial phase of inactivation. The reversal of enzyme activity was obtained by thiol-containing reagents. The loss of enzyme activity was prevented only by NADH and not by other substrates. The dissociation constant for NADH calculated from the decrease in the enzyme inactivation rate was 45 μM. Cyanolysis of the DTNB-modified enzyme with KCN led to the release of 5-thio-2-nitrobenzoate (TNB) accompanied by the formation of thio-cyano enzyme. By correlating the enzyme activity with the formation of thio-cyano derivative it was found that no activity was recovered after kCN treatment. These evidences clearly established the critical involvement of the thiol group in catalysis. Double inhibition studies with PCMs and NEM on octopine dehydrogenase showed that the inactivating reagents bind to the same functional thiol present at the catalytic center. pH-dependent inactivation by PCMS indicated that a group with a p K a value of 7.4 is involved in the loss of enzyme activity. These approaches suggested that at least one thiol group present at the coenzyme-binding domain is essential for the catalytic reaction of octopine dehydrogenase.

Prediction of Structurally Conserved Regions of D-Specific Hydroxy Acid Dehydrogenases by Multiple Alignment with Formate Dehydrogenase

We propose a multiple alignment of the sequence of formate dehydrogenase with the D-specific 2-hydroxy acid dehydrogenases family. Structurally conserved regions are predicted for those sequences corresponding to important regions of the catalytic and the coenzyme binding domains defined from the known three-dimensional structure of the formate dehydrogenase, namely the nicotinamide binding site (βD to βF) and the βA-loop-αB region containing the typical glycine pattern of the adenosine binding site, the catalytic histidine/aspartic acid pair and an arginine probably involved in the interaction with the carboxyl group of the substrate.

Amino acid substitutions at position 47 of human beta 1 beta 1 and beta 2 beta 2 alcohol dehydrogenases affect hydride transfer and coenzyme dissociation rate constants.

Human liver alcohol dehydrogenase isoenzymes beta 1 beta 1 and beta 2 beta 2, in which position 47 in the coenzyme binding domain is an arginine or histidine, respectively, differ remarkably in steady-state kinetics. To understand which catalytic steps affect these kinetics, apparent coenzyme dissociation and association rate constants, and apparent 4-trans-(N,N-dimethylamino)cinnamaldehyde (DACA) hydride transfer rate constants were obtained with stopped-flow kinetics. Enzymes containing site-specific mutations of Arg-47 in beta 1 beta 1 (beta 47R) to His (beta 2 beta 2 or beta 47H), Lys (beta 47K), or Gln (beta 47Q) were studied. Apparent coenzyme dissociation rate constants are greatly affected by substitutions at position 47, in which mutant enzymes with a weak base or a neutral residue at this position (beta 47H and beta 47Q) exhibit faster rate constants than beta 47R and beta 47K. Substitutions at position 47 have less effect on apparent coenzyme association rate constants. The kinetics of NADH association for beta 47H and beta 47Q are consistent with a two-step mechanism in which the bimolecular binding step is coupled to a unimolecular process. These findings indicate that the greater role of position 47 in coenzyme dissociation may occur after a coenzyme-induced isomerization. Substitutions at position 47 also strongly influence apparent DACA hydride transfer rate constants; hydride transfer is faster with mutant enzymes containing weak bases like histidine at this position. Steady-state kinetics, however, reveal that the rate-limiting step of both beta 47R and beta 47H for acetaldehyde reduction and for ethanol oxidation is coenzyme product dissociation. Thus, the different activities of beta 1 beta 1 and beta 2 beta 2 for ethanol oxidation and acetaldehyde reduction are caused primarily by different coenzyme dissociation rates.

Electrostatic interaction energies in lactate dehydrogenase catalysis

A macroscopic approach has been used to calculate electrostatic energies in complexes of L-lactate dehydrogenase with substrates. The different steps of the catalytic mechanism that have been analysed separately are binding of coenzymes and substrates, protonation of the enzyme, the substrate-induced conformational rearrangement of the protein and the chemical transformation of substrate to product. The contributions of the different amino acid residues to each step have been determined from their electrostatic interaction energies. The overall topology of lactate dehydrogenase protein subunit creates, through helix dipoles, two regions of positive potential. One, in the coenzyme-binding domain, stabilises the negatively charged coenzyme pyrophosphate group. The other stabilises both the anionic substrate binding and the developing negative charge excess on the substrate carbonyl in the transition state. The calculated electrostatic fields are those expected from the roles of amino acid side chains which had been previously suggested from site-directed mutagenesis experiments: that is Asp-53 is important in NADH binding, Arg-171 for pyruvate binding and Arg-109 for transition-state stabilisation. His-195, the proton donor/acceptor in catalysis, is stabilised in the protonated state by both Asp-168 and pyruvate. The closure of the active-site loop sequesters the substrate and the nicotinamide ring of the coenzyme in an internal active-site vacuole. The closure process is calculated to be electrostatically unfavourable due to the buried ionic species. Calculation suggests that favourable hydrophobic effects balance unfavourable electrostatic effects and give the precise balance of energies to drive loop (residues 99–112) movement which generates the catalytically competent species.

Crystal structure of NAD-dependent formate dehydrogenase.

The ternary complex of NAD-dependent formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 (enzyme-NAD-azide) has been crystallised in the space group P2(1)2(1)2(1) with cell dimensions a = 11.60 nm, b = 11.33 nm, c = 6.34 nm. There is 1 dimeric molecule/asymmetric unit. An electron density map was calculated using phases from multiple isomorphous replacement at 0.30 nm resolution. Four heavy atom derivatives were used. The map was improved by solvent flattening and molecular averaging. The atomic model, including 2 x 393 amino acid residues, was refined by the CORELS and PROLSQ packages using data between 1.0 nm and 0.30 nm excluding structure factors less than 1 sigma. The current R factor is 27.1% and the root mean square deviation from ideal bond lengths is 4.2 pm. The FDH subunit is folded into a globular two-domain (coenzyme and catalytic) structure and the active centre and NAD binding site are situated at the domain interface. The beta sheet in the FDH coenzyme binding domain contains an additional beta strand compared to other dehydrogenases. The difference in quaternary structure between FDH and the other dehydrogenases means that FDH constitutes a new subfamily of NAD-dependent dehydrogenases: namely the P-oriented dimer. The FDH nucleotide binding region of the structure is aligned with the three dimensional structures of four other dehydrogenases and the conserved residues are discussed. The amino acid residues which contribute to the active centre and which make contact with NAD have been identified.

Characteristics of short‐chain alcohol dehydrogenases and related enzymes

Different short-chain dehydrogenases are distantly related, constituting a protein family now known from at least 20 separate enzymes characterized, but with extensive differences, especially in the C-terminal third of their sequences. Many of the first known members were prokaryotic, but recent additions include mammalian enzymes from placenta, liver and other tissues, including 15-hydroxyprostaglandin, 17 beta-hydroxysteroid and 11 beta-hydroxysteroid dehydrogenases. In addition, species variants, isozyme-like multiplicities and mutants have been reported for several of the structures. Alignments of the different enzymes reveal large homologous parts, with clustered similarities indicating regions of special functional/structural importance. Several of these derive from relationships within a common type of coenzyme-binding domain, but central-chain patterns of similarity go beyond this domain. Total residue identities between enzyme pairs are typically around 25%, but single forms deviate more or less (14-58%). Only six of the 250-odd residues are strictly conserved and seven more are conserved in all but single cases. Over one third of the conserved residues are glycine, showing the importance of conformational and spatial restrictions. Secondary structure predictions, residue distributions and hydrophilicity profiles outline a common, N-terminal coenzyme-binding domain similar to that of other dehydrogenases, and a C-terminal domain with unique segments and presumably individual functions in each case. Strictly conserved residues of possible functional interest are limited, essentially only three polar residues. Asp64, Tyr152 and Lys156 (in the numbering of Drosophila alcohol dehydrogenase), but no histidine or cysteine residue like in the completely different, classical medium-chain alcohol dehydrogenase family. Asp64 is in the suggested coenzyme-binding domain, whereas Tyr152 and Lys156 are close to the center of the protein chain, at a putative inter-domain, active-site segment. Consequently, the overall comparisons suggest the possibility of related mechanisms and domain properties for different members of the short-chain family.

Autonomous folding and coenzyme binding of the excised pyridoxal 5'-phosphate binding domain of aspartate aminotransferase from Escherichia coli

The coenzyme (PLP) binding domain (residues 47-329) of the dimeric aspartate aminotransferase from Escherichia coli was produced separately by recombinant DNA methods. It folded autonomously both in vivo and in vitro, that is, independently of the native N- and C-terminal extensions that combine to form the small domain of eAAT. The PLP-domain had one binding site for PLP of relatively high affinity involving a covalent bond to the protein. It was monomeric, although the major subunit-subunit interface at the 2-fold symmetry axis remained unchanged. This effect appears to be due mainly to the absence of the N-terminal extension that contains hydrophobic residues, which interact with the PLP-domain of the second subunit in the wild-type dimer. Judged by circular dichroism, fluorescence, and HPLC gel filtration at increasing concentrations of guanidinium chloride, the PLP-domain underwent a three-state unfolding transition (M' in equilibrium M'* in equilibrium U') involving a compact intermediate M'*. This behavior parallels the unfolding of the dissociated native monomer of cAAT.

Molecular evolution of the zinc-containing long-chain alcohol dehydrogenase genes.

Phylogenetic relationships and rates of nucleotide substitution were studied for alcohol dehydrogenase (ADH) genes by using DNA sequences from mammals and plants. Mammalian ADH sequences include the three class I genes and a class II gene from humans and one gene each from baboon, rat, and mouse. Plant sequences include two ADH genes each from maize and rice, three genes from barley, and one gene each from wheat and two dicots, Arabidopsis and pea. Phylogenetic trees show that relationships among ADH genes are generally consistent with taxonomic relationships: mammalian and plant ADH genes are classified into two distinct groups; primate class I genes are clustered; and two dicot sequences are clustered separately from monocot sequences. Accelerated evolution has been detected among the duplicated ADH genes in plants, in which synonymous substitutions occurred more often within the coenzyme-binding domain than within the catalytic domains.