Extensive variations and basic features in the alcohol dehydrogenase-sorbitol dehydrogenase family

Isolation of extracellular fluids reveals novel secreted bioactive proteins from muscle and fat tissues

Proteins are secreted from cells to send information to neighboring cells or distant tissues. Because of the highly integrated nature of energy balance systems, there has been particular interest in myokines and adipokines. These are challenging to study through proteomics because serum or plasma contains highly abundant proteins that limit the detection of proteins with lower abundance. We show here that extracellular fluid (EF) from muscle and fat tissues of mice shows a different protein composition than either serum or tissues. Mass spectrometry analyses of EFs from mice with physiological perturbations, like exercise or cold exposure, allowed the quantification of many potentially novel myokines and adipokines. Using this approach, we identify prosaposin as a secreted product of muscle and fat. Prosaposin expression stimulates thermogenic gene expression and induces mitochondrial respiration in primary fat cells. These studies together illustrate the utility of EF isolation as a discovery tool for adipokines and myokines.

Thermotoga maritima TM0298 is a highly thermostable mannitol dehydrogenase

Thermotoga maritima TM0298 is annotated as an alcohol dehydrogenase, yet it shows high identity and similarity to mesophilic mannitol dehydrogenases. To investigate this enzyme further, its gene was cloned and expressed in Escherichia coli. The purified recombinant enzyme was most active on fructose and mannitol, making it the first known hyperthermophilic mannitol dehydrogenase. T. maritima mannitol dehydrogenase (TmMtDH) is optimally active between 90 and 100 degrees C and retains 63% of its activity at 120 degrees C but shows no detectable activity at room temperature. Its kinetic inactivation follows a first-order mechanism, with half-lives of 57 min at 80 degrees C and 6 min at 95 degrees C. Although TmMtDH has a higher V (max) with NADPH than with NADH, its catalytic efficiency is 2.2 times higher with NADH than with NADPH and 33 times higher with NAD(+) than with NADP(+). This cofactor specificity can be explained by the high density of negatively charged residues (Glu193, Asp195, and Glu196) downstream of the NAD(P) interaction site, the glycine motif. We demonstrate that TmMtDH contains a single catalytic zinc per subunit. Finally, we provide the first proof of concept that mannitol can be produced directly from glucose in a two-step enzymatic process, using a Thermotoga neapolitana xylose isomerase mutant and TmMtDH at 60 degrees C.

Optimized synthesis of L-sorbose by C(5)-dehydrogenation of D-sorbitol with Gluconobacter oxydans

The optimization of L-sorbose synthesis by regiospecific dehydrogenation of D-sorbitol using Gluconobacter oxydans is reported. The current L-sorbose production processes that are based on G. oxydans and other bacterial strains are suboptimal as to yield and rate of L-sorbose synthesis. One reason for these problems is the toxicity that is induced by the substrate D-sorbitol when used in concentrations of >10% (w/v). This phenomenon significantly limits the potentials of L-sorbose production from an industrial point of view. The goal of this study was to develop a fast production process that yields L-sorbose in stoichiometric amounts starting from D-sorbitol concentrations that exceed 10% (w/v). A gradual improvement of the inoculum build-up procedure, culture medium composition, and process parameters ultimately led to a theoretically maximal L-sorbose productivity (200 g L(-1) of L-sorbose from 200 g L(-1) of D-sorbitol in 28 h of fermentation) using a Gluconobacter oxydans mutant strain that was selected under conditions of substrate inhibition. Because the D-sorbitol/L‐sorbose bioconversion is used to mass-produce vitamin C, the procedure reported here will contribute to a more efficient and more economic synthesis of vitamin C.

Molecular basis for thermoprotection in Bemisia: structural differences between whitefly ketose reductase and other medium-chain dehydrogenases/reductases

The silverleaf whitefly (Bemisia argentifolii, Bellows and Perring) accumulates sorbitol as a thermoprotectant in response to elevated temperature. Sorbitol synthesis in this insect is catalyzed by an unconventional ketose reductase (KR) that uses NADPH to reduce fructose. A cDNA encoding the NADPH-KR from adult B. argentifolii was cloned and sequenced to determine the primary structure of this enzyme. The cDNA encoded a protein of 352 amino acids with a calculated molecular mass of 38.2 kDa. The deduced amino acid sequence of the cDNA shared 60% identity with sheep NAD(+)-dependent sorbitol dehydrogenase (SDH). Residues in SDH involved in substrate binding were conserved in the whitefly NADPH-KR. An important structural difference between the whitefly NADPH-KR and NAD(+)-SDHs occurred in the nucleotide-binding site. The Asp residue that coordinates the adenosyl ribose hydroxyls in NAD(+)-dependent dehydrogenases (including NAD(+)-SDH), was replaced by an Ala in the whitefly NADPH-KR. The whitefly NADPH-KR also contained two neutral to Arg substitutions within four residues of the Asp to Ala substitution. Molecular modeling indicated that addition of the Arg residues and loss of the Asp decreased the electric potential of the adenosine ribose-binding pocket, creating an environment favorable for NADPH-binding. Because of the ability to use NADPH, the whitefly NADPH-KR synthesizes sorbitol under physiological conditions, unlike NAD(+)-SDHs, which function in sorbitol catabolism.

Sorbitol dehydrogenase of Drosophila. Gene, protein, and expression data show a two-gene system

The Drosophila melanogaster sorbitol dehydrogenase (SDH) is characterized as a two-enzyme system of the medium chain dehydrogenase/reductase family (MDR). The SDH-1 enzyme has an enzymology with Km and kcat values an order of magnitude higher than those for the human enzyme but with a similar kcat/Km ratio. It is a tetramer with identical subunits of approximately 38 kDa. At the genomic level, two genes, Sdh-1 and Sdh-2, have a single transcriptional start site and no functional TATA box. Expression is greater in larvae and adults than in pupae, where it is very low. At all three stages, Sdh-1 constitutes the major transcript. Sdh-1 and Sdh-2 genes were located at positions 84E-F and 86D in polytene chromosomes. The deduced amino acid sequences of the two genes show 90% residue identity. Evaluation of the sequence and modeling of the structure toward that of class I alcohol dehydrogenase (ADH) show altered loop and gap arrangements as in mammalian SDH and establishes that SDH, despite gene multiplicity and larger variability than the "constant" ADH of class III, is an enzyme conserved over wide ranges.

The rkpGHI and -J genes are involved in capsular polysaccharide production by Rhizobium meliloti

The first complementation unit of the fix-23 region of Rhizobium meliloti, which comprises six genes (rkpAB-CDEF) exhibiting similarity to fatty acid synthase genes, is required for the production of a novel type of capsular polysaccharide that is involved in root nodule development and structurally analogous to group II K antigens found in Escherichia coli (G. Petrovics, P. Putnoky, R. Reuhs, J. Kim, T. A. Thorp, K. D. Noel, R. W. Carlson, and A. Kondorosi, Mol. Microbiol. 8:1083-1094, 1993; B. L. Reuhs, R. W. Carlson, and J. S. Kim, J. Bacteriol. 175:3570-3580, 1993). Here we present the nucleotide sequence for the other three complementation units of the fix-23 locus, revealing the presence of four additional open reading frames assigned to genes rkpGHI and -J. The putative RkpG protein shares similarity with acyltransferases, RkpH is homologous to short-chain alcohol dehydrogenases, and RkpJ shows significant sequence identity with bacterial polysaccharide transport proteins, such as KpsS of E. coli. No significant homology was found for RkpI. Biochemical and immunological analysis of Tn5 derivatives for each gene demonstrated partial or complete loss of capsular polysaccharides from the cell surface; on this basis, we suggest that all genes in the fix-23 region are required for K-antigen synthesis or transport.

New alcohol dehydrogenases for the synthesis of chiral compounds

The enantioselective reduction of carbonyl groups is of interest for the production of various chiral compounds such as hydroxy acids, amino acids, hydroxy esters, or alcohols. Such products have high economic value and are most interesting as additives for food and feed or as building blocks for organic synthesis. Enzymatic reactions or biotransformations with whole cells (growing or resting) for this purpose are described. Although conversions with whole cells are advantageous with respect to saving expensive isolation of the desired enzymes, the products often lack high enantiomeric excess and the process results in low time-space-yield. For the synthesis of chiral alcohols, only lab-scale syntheses with commercially available alcohol dehydrogenases have been described yet. However, most of these enzymes are of limited use for technical applications because they lack substrate specificity, stability (yeast ADH) or enantioselectivity (Thermoanaerobium brockii ADH). Furthermore, all enzymes so far described are forming (S)-alcohols. Quite recently, we found and characterized several new bacterial alcohol dehydrogenases, which are suited for the preparation of chiral alcohols as well as for hydroxy esters in technical scale. Remarkably, of all these novel ADHs the (R)-specific enzymes were found in strains of the genus Lactobacillus. Meanwhile, these new enzymes were characterized extensively. Protein data (amino acid sequence, bound cations) confirm that these catalysts are novel enzymes. (R)-specific as well as (S)-specific ADHs accept a broad variety of ketones and ketoesters as substrates. The applicability of alcohol dehydrogenases for chiral syntheses as an example for the technical use of coenzyme-dependent enzymes is demonstrated and discussed in this contribution. In particular NAD-dependent enzymes coupled with the coenzyme regeneration by formate dehydrogenase proved to be economically feasible for the production of fine chemicals.

Structure of the Bombyx sorbitol dehydrogenase gene: a possible alternative use of the promoter

In an initial effort to understand the molecular mechanism of how low temperature induces sorbitol dehydrogenase gene expression in diapause eggs of the silkworm, the sorbitol dehydrogenase gene was isolated from a Bombyx genomic library using a cDNA encoding the Bombyx homologue of mammalian sorbitol dehydrogenase as a probe. The gene extended for about 10 kb, consisting of eight exons and seven introns. Four TATA motifs were found in the 5' upstream region of the gene, without CCAAT. AATTAA, instead of AATAAA, was localized in the upstream region of the polyadenylation site. Although a single copy of this gene was present per haploid genome, 1.2 kb and 1.1 kb transcripts were found from yolk cells in diapause eggs and from larval fat-body cells, respectively. The two major transcription initiation sites corresponding to both transcripts were localized at 355 and 226 base pairs upstream from the transition start site, indicating an alternative use of promoter. The 5'-upstream region of the gene contained a consensus sequence, TGA(A/T)AA(A/G/T), that has been found in insect genes expressed mainly in larval and pupal fat bodies. It also contained three kinds of sequences similar to cis-elements recognized by members of the steroid receptor superfamily, such as chicken ovalbumin upstream promoter transcription factor (COUP-TF)/Drosophila Seven up (SVP), Drosophila hormone receptor 39 (DHR39) and Bombyx fushi tarazu transcriptional factor 1 (BmFTZ-F1).

Structural organization of the human sorbitol dehydrogenase gene (SORD)

The primary structure of human sorbitol dehydrogenase (SORD) was determined by cDNA and genomic cloning. The nucleotide sequence of the mRNA covers 2471 bp including an open reading frame that yields a protein of 356 amino acid residues. The gene structure of SORD spans approximately 30 kb divided into 9 exons and 8 introns. The gene was localized to chromosome 15q21.1 by in situ hybridization. Two transcription initiation sites were detected. Three Sp1 sites and a repetitive sequence (CAAA)5 were observed in the 5' noncoding region; no classical TATAA or CCAAT elements were found. The related alcohol dehydrogenases and zeta-crystallin have the same gene organization split by 8 introns, but no splice points coincide between SORD and these gene types. The deduced amino acid sequence of the SORD structure differs at a few positions from the directly determined protein sequence, suggesting allelic forms of the enzyme. High levels of SORD transcripts were observed in lens and kidney, as judged from Northern blot analysis.

The crystal structure of glucose dehydrogenase from Thermoplasma acidophilum

BACKGROUND

The archaea are a group of organisms distinct from bacteria and eukaryotes. Structures of proteins from archaea are of interest because they function in extreme environments and because structural studies may reveal evolutionary relationships between proteins. The enzyme glucose dehydrogenase from the thermophilic archaeon Thermoplasma acidophilum is of additional interest because it is involved in an unusual pathway of sugar metabolism.

RESULTS

We have determined the crystal structure of this glucose dehydrogenase to 2.9 A resolution. The monomer comprises a central nucleotide-binding domain, common to other nucleotide-binding dehydrogenases, flanked by the catalytic domain. Unexpectedly, we observed significant structural homology between the catalytic domain of horse liver alcohol dehydrogenase and T. acidophilum glucose dehydrogenase.

CONCLUSIONS

The structural homology between glucose dehydrogenase and alcohol dehydrogenase suggests an evolutionary relationship between these enzymes. The quaternary structure of glucose dehydrogenase may provide a model for other tetrameric alcohol/polyol dehydrogenases. The predicted mode of nucleotide binding provides a plausible explanation for the observed dual-cofactor specificity, the molecular basis of which can be tested by site-directed mutagenesis.

Zinc coordination in mammalian sorbitol dehydrogenase. Replacement of putative zinc ligands by site-directed mutagenesis

Rat sorbitol dehydrogenase was expressed in Escherichia coli and purified to homogeneity, resulting in a protein with a specific activity of 4.7 U/mg, close to that of the enzyme isolated from mammalian liver. A Glu residue has been postulated to replace the Cys of alcohol dehydrogenase as a ligand to the active-site zinc atom of sorbitol dehydrogenase. This Glu (position 155 in the rat enzyme) was mutated both to Cys, in order to mimic the alcohol dehydrogenase relationships, and to Ala, as a control. A third mutation, Cys164 to Ala, was also performed since Cys has also been considered as a possible zinc ligand. With Ala at position 155, an inactive enzyme was obtained, showing that correct active-site relationships have been destroyed. With Cys at position 155, the enzyme is still partly active, but rapidly looses activity unless stabilized by the addition of ZnSO4. The catalytic efficiency in the oxidation of sorbitol is 120-fold less than that of the native form, and reduction of fructose is lost completely. In contrast, the activity of the Cys164Ala mutant is comparable with that of the native enzyme and, in fact, even increased in the oxidation of sorbitol. Combined, the results strongly suggest that Glu155 is a ligand to the active-site zinc atom. Zinc analysis of the different variants of sorbitol dehydrogenase establishes that all contain one atom of zinc/subunit, also when the catalytic function is lost. Apparently, zinc remains coordinated even after replacement with an amino acid residue (Ala) unable to ligand metal atoms.

A cold-inducible Bombyx gene encoding a protein similar to mammalian sorbitol dehydrogenase. Yolk nuclei-dependent gene expression in diapause eggs

To facilitate the study of the induction of sorbitol dehydrogenase by acclimation to 5 degrees C in diapause eggs of the silkworm, Bombyx mori, two cDNA libraries from eggs and larval fat bodies were screened with anti-(sorbitol dehydrogenase) serum, and a positive cDNA was cloned from the fat-body cDNA library. 1039 nucleotides determined from the cDNA corresponded to a protein-coding region consisting of 346 amino acids. The missing regions (containing two amino acids at the 5' end and a stop codon at the 3' end) were supplemented with the genome sequence. The deduced amino-acid sequence had 45-47% identity with mammalian sorbitol dehydrogenases. The results led us to conclude that the cDNA for a Bombyx homolog of mammalian sorbitol dehydrogenase was isolated, which was designated as BmSDH. Analyses of Northern hybridization and reverse transcription/polymerase chain reaction showed that the transcript of BmSDH occurred after chilling for 40-50 days when the diapause eggs were exposed to 5 degrees C from two days after oviposition to break the diapause. The changing pattern in the amount of BmSDH transcript was well correlated with those in the activity of sorbitol dehydrogenase and the amount of the enzyme protein in diapause eggs. Further, the transcript of BmSDH was localized in yolk cells. The results indicate that the yolk nuclei-dependent gene expression of BmSDH is induced by acclimation to 5 degrees C in diapause eggs.

Affinity labelling of sorbitol dehydrogenase from sheep liver with alpha-bromo-beta-(5-imidazolyl)propionic acid

The metal-directed alkylating agent DL-alpha-bromo-beta-(5- imidazolyl)propionic acid (BrImPpOH) is shown to be an affinity-labelling reagent for sheep liver sorbitol dehydrogenase (SDH). As previously found for horse liver alcohol dehydrogenase (ADH), it modifies a cysteine ligand to the active-site zinc. In this case it is selectively incorporated (over 90%) at Cys43 in each of the four polypeptide chains/protomers of sheep liver SDH. Incorporated reagent and residual activity correlated. The first order inactivation constant, K2, and KEI, the dissociation constant for SDH and BrImPpOH, have been determined at different pH. The reactivity of BrImPpOH for SDH is higher than that for horse liver and yeast ADH. The protection of SDH against BrImPpOH inactivation by buffers and other molecules shows some similarities to that with horse liver ADH. However, sheep liver SDH bound BrImPpOH, imidazole and phosphate ions much weaker than liver ADH. The pKa values from the plot of log (k2/KEI) against pH are approximately 7.0 and 8.8-8.9. The former pKa value probably represents ionization of an imidazole group and the latter the zinc/water ionization in SDH. These pKa values are similar to those found for horse liver ADH. They are apparently not noticeably influenced by a second cysteine ligand in liver ADH being replaced by a proposed glutamic acid residue as a ligand to the catalytic zinc in SDH. The plot of logk2 against pH shows pKa values around 7.0 and 9.2 for the SDH-BrImPpOH-complex. The pKa of 7.0 is the same as for log(k2/KEI), and indicates no significant perturbation due to the binding of BrImPpOH to SDH. The pKa around 9.2 indicates perturbation of the zinc/water ionization or the ionization of Cys43.

The kinetic mechanism of sheep liver sorbitol dehydrogenase

The relations between the kinetic parameters for both sorbitol oxidation and fructose reduction by sheep liver sorbitol dehydrogenase show that a Theorell-Chance compulsory order mechanism operates from pH 7.4 to 9.9. This is supported by many parallels with the kinetics of horse liver alcohol dehydrogenase, which operates by this classical mechanism. An isotope-exchange study using D-(2H8)sorbitol confirmed the existence of ternary complexes and that, under maximum velocity conditions, their interconversion is not rate-determining. Substrate inhibition at high concentrations of D-sorbitol or D-fructose confirmed rate-determining enzyme--coenzyme product dissociation, slowed by the existence of more stable abortive ternary enzyme-coenzyme product complexes with substrate. The effect of the inhibitor/activator 2,2,2-tribromoethanol showed the existence of enzyme-NAD-CBr3CH2OH complexes inhibiting the first phase of reaction and enzyme-NADH-CBr3CH2OH complexes dissociating more rapidly than the usual rate-determining enzyme-NADH coenzyme product dissociation in the final phase. Inhibition studies with dithiothreitol also confirmed an ordered binding of coenzymes and second substrates to sorbitol dehydrogenase. Neither D-sorbitol nor D-fructose had any effect on enzyme inactivation by the affinity labelling reagent DL-2-bromo-3-(5-imidazolyl)propionic acid, thus giving no evidence for their existence as binary enzyme-substrate complexes. Several alternative polyol substrates for sorbitol dehydrogenase gave the same maximum velocity as sorbitol. This indicated a common rate-limiting binary enzyme-NADH product dissociation and a similarity of mechanism. An enzyme assay for pH 7.0 and 9.9 is given which enables the concentration of sorbitol dehydrogenase to be determined from initial rate measurements of enzyme activity.

Structural features of stomach aldehyde dehydrogenase distinguish dimeric aldehyde dehydrogenase as a 'variable' enzyme. 'Variable' and 'constant' enzymes within the alcohol and aldehyde dehydrogenase families

Stomach aldehyde dehydrogenase was structurally evaluated by analysis of peptide fragments of the human enzyme and comparisons with corresponding parts from other characterized aldehyde dehydrogenases. The results establish a large part of the structure, confirming that the stomach enzyme is identical to the inducible or tumor-derived dimeric aldehyde dehydrogenase. In addition, species variations between identical sets of different aldehyde and alcohol dehydrogenases reveal that stomach aldehyde dehydrogenase exhibits a fairly rapid rate of evolutionary changes, similar to that for the likewise 'variable' classical alcohol dehydrogenase, sorbitol dehydrogenase, and cytosolic aldehyde dehydrogenase but in contrast to the 'constant' class III alcohol dehydrogenase and mitochondrial aldehyde dehydrogenase. This establishes that rates of divergence in the aldehyde and alcohol dehydrogenases are unrelated to subunit size or quaternary structure, highlights the unique nature of class III alcohol dehydrogenase, and positions the stomach aldehyde dehydrogenase in a group with more ordinary features.

Variability within mammalian sorbitol dehydrogenases. The primary structure of the human liver enzyme

The primary structure of sorbitol dehydrogenase from human liver has been determined by peptide analysis in order to relate the variability of this enzyme to that of the others within the alcohol dehydrogenase family. The structure obtained reveals 355 residues with an acyl-blocked N-terminus and an unexpected microheterogeneity at position 237 (Gln/Leu). The residue identity between sheep and human liver sorbitol dehydrogenase is 89%. This variability is similar to that of class I alcohol dehydrogenases, but distinctly different from that of class III alcohol dehydrogenases, the structures of which are much more conserved. Consequently, class III alcohol dehydrogenase is thus far unique within this family of dehydrogenases, suggesting a particularly strict requirement for that structure. The variability within sorbitol dehydrogenase involves all segments of the molecule but is largely at surface positions and clusters in one such region, covering positions 214-240, corresponding to a segment of the coenzyme-binding domain. Ligands to the active-site zinc and most residues lining the coenzyme-binding and substrate-binding pockets are conserved. However, provided conformational models are reliable, a charge difference may affect the interactions at the inner part of the substrate pocket, another charge difference may affect the interdomain region, and a size difference the adenine pocket. The primary structure of human liver sorbitol dehydrogenase further shows that the absence of three of the four ligands to a second zinc atom present in alcohol dehydrogenases is a general property of sorbitol dehydrogenase.

Glucose-6-phosphate dehydrogenase. Characteristics revealed by the rat liver enzyme structure

The primary structure of glucose-6-phosphate dehydrogenase from rat liver has been determined, showing the mature polypeptide to consist of 513 amino acid residues, with an acyl-blocked N-terminus. This structure is homologous to those of both other eutherian and marsupial mammals (human and opossum), thus characterizing a mammalian type enzyme to which the human form, notwithstanding its large number of genetic variants, conforms. The mammalian type differs from the fruit fly enzyme by about 50%. Known mutant forms exhibit further differences, widely distributed along the polypeptide chain. Structural patterns show glucose-6-phosphate dehydrogenases to consist of a few variable regions intermixed with relatively constant segments.

Nonpolar interactions in the modification of an essential sulfhydryl of sorbitol dehydrogenase by N-alkylmaleimides

A series of N-alkylmaleimides varying in chainlength from N-methyl- to N-octylmaleimide inclusive was shown to effectively inactivate sheep liver sorbitol dehydrogenase at pH 7.5 and 25 degrees C. The apparent second-order rate constants for inactivation increased with increasing chainlength of the N-alkylmaleimide used. Positive chainlength effects were also indicated by the Kd values for the N-ethyl and N-heptyl derivatives obtained from studies of the saturation kinetics observed for inactivation of the enzyme at high concentrations of these maleimides. The complete inactivation of sorbitol dehydrogenase was demonstrated to occur through the selective covalent modification of one cysteine residue per subunit of enzyme. The stoichiometry of enzyme inactivation was supported on the one hand by fluorescence titration with fluorescein mercuric acetate of the native and the inactivated enzyme, and, on the other hand, by the simultaneous inactivation of the enzyme with selective modification of one sulfhydryl per subunit by N-[p-(2-benzoxazolyl)phenyl]maleimide. Protection of the enzyme from N-alkylmaleimide inactivation was observed with the binding of NADH, whereas both NAD and sorbitol were ineffective as protecting ligands. Diazotized 3-aminopyridine adenine dinucleotide, in contrast to previous studies of this reagent with yeast alcohol dehydrogenase and rabbit muscle glycerophosphate dehydrogenase, did not function as a site-labeling reagent for sorbitol dehydrogenase.

L-histidinol dehydrogenase, a Zn2+-metalloenzyme

The enzymatic activity of L-histidinol dehydrogenase from Salmonella typhimurium was stimulated by the inclusion of 0.5 mM MnCl2 in the assay medium. At pH 9.2 the stimulation was correlated with binding of 1 g-atom of 54Mn2+/mol dimer, KD = 37 microM. ZnCl2, which prevented the MnCl2 stimulation, also bound to the enzyme, 1.2 g-atom/mol dimer, KD = 51 microM, and prevented Mn2+ binding. Enzyme activity was lost when histidinol dehydrogenase was incubated in 8 M urea. Reactivation was observed when urea-denatured enzyme was diluted into buffer containing 2-mercaptoethanol but required either MnCl2 or ZnCl2. Histidinol dehydrogenase was inactivated by the transition metal chelator 1,10-phenanthroline or by high levels of 2-mercaptoethanol. The nonchelating 1,7-phenanthroline was not an inactivator, and inactivation by either 1,10-phenanthroline or 2-mercaptoethanol was prevented by MnCl2. Enzyme inactivated by 1,10-phenanthroline could be reactivated by addition of MnCl2 or ZnCl2 in the presence of 2-mercaptoethanol. Reactivation was correlated with the binding of 1.5 g-atom 54Mn2+/mol dimer. Atomic absorption analysis of the native enzyme indicated the presence of 1.65 g-atom Zn/mol dimer, and no Mn was detected. The results demonstrate, therefore, that histidinol dehydrogenase contains two metal binding sites per enzyme dimer, which normally bind Zn2+, but which may bind Mn2+ while retaining enzyme function. Histidinol dehydrogenase is thus the third NAD-linked oxidoreductase in which Zn2+ fulfills an essential structural and/or catalytic role.

The primary structure of alcohol dehydrogenase from Drosophila lebanonensis. Extensive variation within insect 'short-chain' alcohol dehydrogenase lacking zinc

Insect alcohol dehydrogenase is highly different from the well-known yeast and mammalian alcohol dehydrogenases. The enzyme from Drosophila lebanonensis has now been characterized by protein analysis and was found to have a 254-residue protein chain with an acetyl-blocked N-terminal Met. Comparisons with the structures of the enzyme from other species allows judgement of the extent of variability within the insect alcohol dehydrogenases. They have diverged to a considerable extent; two forms analyzed at the protein level differ at 18% of all residues, and all the known Drosophila alcohol dehydrogenase structures reveal differences at 72 positions. Some deviations, against a background similarity, in the extent of changes are noted among the parts corresponding to different exons. The structural variation within Drosophila is about as large as the one for the mammalian zinc-containing alcohol dehydrogenase. Consequently, the results illustrate Drosophila relationships and establish great variations also for group of alcohol dehydrogenases lacking zinc.

Rat liver alcohol dehydrogenase of class III. Primary structure, functional consequences and relationships to other alcohol dehydrogenases

The amino acid sequence of alcohol dehydrogenase of class III from rat liver (the enzyme ADH-2) has been determined. This type of structure is quite different from those of both the class I and the class II alcohol dehydrogenases. The rat class III structure differs from the rat and human class I structures by 133-138 residues (exact value depending on species and isozyme type); and from that of human class II by 132 residues. In contrast, the rat/human species difference within the class III enzymes is only 21 residues. The protein was carboxymethylated with iodo[2(14)C]acetate, and cleaved with CNBr and proteolytic enzymes. Peptides purified by exclusion chromatography and reverse-phase high-performance liquid chromatography were analyzed by degradation with a gas-phase sequencer and with the manual 4-N,N-dimethylaminoazobenzene-4'-isothiocyanate double-coupling method. The protein chain has 373 residues with a blocked N terminus. No evidence was obtained for heterogeneity. The rat ADH-2 enzyme of class III contains an insertion of Cys at position 60 in relation to the class I enzymes, while the latter alcohol dehydrogenase in rat (ADH-3) has another Cys insertion (at position 111) relative to ADH-2. The structure deduced explains the characteristic differences of the class III alcohol dehydrogenase in relation to the other classes of alcohol dehydrogenase, including a high absorbance, an anodic electrophoretic mobility and special kinetic properties. The main amino acid substitutions are found in the catalytic domain and in the subunit interacting segments of the coenzyme-binding domain, the latter explaining the lack of hybrid dimers between subunits of different classes. Several substitutions provide an enlarged and more hydrophilic substrate-binding pocket, which appears compatible with a higher water content in the pocket and hence could possibly explain the higher Km for all substrates as compared with the corresponding values for the class I enzymes. Finally the class III structure supports evolutionary relationships suggesting that the three classes constitute clearly separate enzymes within the group of mammalian zinc-containing alcohol dehydrogenases.

Computer-graphics interpretations of residue exchanges between the alpha, beta and gamma subunits of human-liver alcohol dehydrogenase class I isozymes

Three-dimensional models of human alcohol dehydrogenase subunits have been constructed, based on the homologous horse enzyme, with computer graphics. All types of class I subunits (alpha, beta, and gamma) and the major allelic variants (beta 1/beta 2 and gamma 1/gamma 2) have been studied. Residue differences between the E-type subunit of the horse enzyme and any of the subunits of the human isozymes occur at 64 positions, about half of which are isozyme-specific. About two thirds of the substitutions are at the surface and all differences can be accommodated in highly conserved three-dimensional structures. The model of the gamma isozyme is most similar to the crystallographically analyzed horse liver E-type alcohol dehydrogenase, and has all the functional residues identical to those of the E subunit except for one which is slightly smaller: Val-141 in the substrate pocket. The residues involved in coenzyme binding are generally conserved between the horse enzyme and the alpha, beta, and gamma types of the human enzyme. In contrast, single exchanges of these residues are the ones involved in the major allelic differences (beta 1 versus beta 2 and gamma 1 versus gamma 2), which affects the overall rate of alcohol oxidation since NADH dissociation is the rate-determining step. Residue 47 is His in beta 2 and Arg in the beta 1, gamma 1, and gamma 2 subunits, and in horse liver alcohol dehydrogenase. Both His and Arg can make a hydrogen bond to a phosphate oxygen atom of NAD; hence the lower turnover rate of beta 1 apparently derives from a charge effect. The substitution to Gly in the alpha subunit results in one less hydrogen bond in NAD binding, and consequently in rapid dissociation. This may explain why the overall rate is an order of magnitude faster than that of beta 1. The important difference between gamma 1 and gamma 2 is an exchange at position 271 from Arg to Gln which can give a hydrogen bond from Gln in gamma 2 to the adenine of NAD. The tighter binding to gamma 2 can account for the slower overall catalytic rate in this isozyme. The kinetics and interactions of cyclohexanol and benzyl alcohol with the isozymes were judged by docking experiments using an interactive fitting program.(ABSTRACT TRUNCATED AT 400 WORDS)

Characteristics of alcohol/polyol dehydrogenases. The zinc-containing long-chain alcohol dehydrogenases

Sixteen characterized alcohol dehydrogenases and one sorbitol dehydrogenase have been aligned. The proteins represent two formally different enzyme activities (EC 1.1.1.1 and EC 1.1.1.14), three different types of molecule (dimeric alcohol dehydrogenase, tetrameric alcohol dehydrogenase, tetrameric sorbitol dehydrogenase), metalloproteins with different zinc contents (1 or 2 atoms per subunit), and polypeptide chains from different kingdoms and orders (mammals, higher plants, fungus, yeasts). Present comparisons utilizing all 17 forms reveal extensive variations in alcohol dehydrogenase, but with evolutionary changes that are of the same order in different branches and at different times. They emphasize the general importance of particular residues, suggesting related overall functional constraints in the molecules. The comparisons also define a few coincidences between intron positions in the genes and gap positions in the gene products. Only 22 residues are strictly conserved; half of these are Gly, and most of the remaining ones are Pro or acidic residues. No basic residue, no straight-chain hydrophobic residues, no aromatic residues, and essentially no branched-chain or polar neutral residues are invariable. Tentative consensus sequences were calculated, defining 13 additional residues likely to be typical of but not invariant among the alcohol dehydrogenases. These show a predominance of Val, charged residues, and Gly. Combined, the comparisons, which are particularly relevant to the data base for protein engineering, illustrate the requirements for functionally important binding interactions, and the extent of space restrictions in proteins with related overall conformations and functions.

Immunological cross-reactivity of alcohol dehydrogenase (ADH) isozymes with rabbit immune sera against horse and human ADH subunits

Rabbit immune sera raised against denatured forms of horse liver alcohol dehydrogenase and of human ADH5 isozyme were found to react with the denatured subunits of all the human ADH isozymes regardless of their class. The immune serum against the human ADH isozyme cross-reacted also with horse ADH subunits and, at appropriate dilutions, both the immune sera reacted with denatured yeast ADH, suggesting that common structures have been preserved in these molecules over a long evolutionary period. The immune sera partially reacted also with the respective antigens in their native conformation, indicating that some 'sequential' epitopes are expressed on the surface of the folded proteins.

cDNA and protein structure for the alpha subunit of human liver alcohol dehydrogenase

Two cDNA clones for human liver alcohol dehydrogenase (ADH) were identified, together covering 1450 nucleotides that contain the cDNA sequence of the ADH1 locus and include a coding region of 1122 nucleotides for the alpha subunit of the enzyme. In parallel, direct peptide analyses of the carboxymethylated protein also established most of the amino acid sequence. Nucleotide and peptide data were in complete agreement and show exchanges at 24 positions in the alpha relative to the beta subunit. One of the cDNA clones had a 139-nucleotide internal deletion at a position of possible interest in relation to mRNA processing, ancestral connections, or DNA replication. The structure of the alpha subunit is homologous to that of the beta and gamma subunits but has many exchanges, also of functionally important residues, explaining the different enzymatic properties. In total, 35 of 374 amino acid residues differ between the class I isozymes, and the substitutions add an extra SH group in the alpha subunit. Only in the beta-pleated sheet region of the coenzyme-binding domain is almost complete lack of substitutions noted, illustrating the importance of this region. In contrast, the active site region is far less conserved. However, similar exchanges of functional significance have also been found in distantly related alcohol and polyol dehydrogenases.

Intron-dependent evolution of the nucleotide-binding domains within alcohol dehydrogenase and related enzymes

It has been suggested that the intron/exon structure of a gene corresponds to its evolutionary history. Accordingly, early in evolution DNA segments encoding short functional polypeptides may have been rearranged (exon-shuffling) to create full-length genes and RNA splicing may have been developed to remove intervening sequences (introns) in order to preserve translational reading frames. A conflicting viewpoint would be that introns were randomly inserted into previously uninterrupted genes after their initial evolutionary development. If so, the sites of introns would be unlikely to consistently reflect the domain structure of the protein. To address this question, the intron/exon structure of the gene encoding human alcohol dehydrogenase (ADH) was determined and compared to the gene structures for other ADHs and related proteins, all of which possess nucleotide-binding domains. Our results indicate that the introns in the nucleotide-binding domains of all the genes examined do indeed fall at positions which separate the short functional polypeptides (i.e. beta strands) which are believed to comprise this domain. We argue that our data is most easily explained by the hypothesis that introns were present in an ancestral nucleotide-binding domain which was later rearranged by exon-shuffling to form the various dehydrogenases and kinases which utilize such a domain.

Three human alcohol dehydrogenase subunits: cDNA structure and molecular and evolutionary divergence

Class I human alcohol dehydrogenase (ADH; alcohol:NAD+ oxidoreductase, EC 1.1.1.1) consists of several homo- and heterodimers of alpha, beta, and gamma subunits that are governed by the ADH1, ADH2, and ADH3 loci. We previously cloned a full length of cDNA for the beta subunit, and the complete sequence of 374 amino acid residues was established. cDNAs for the alpha and gamma subunits were cloned and characterized. A human liver cDNA library, constructed in phage lambda gt11, was screened by using a synthetic oligonucleotide probe that was matched to the gamma but not to the beta sequence. Clone pUCADH gamma 21 and clone pUCADH alpha 15L differed from beta cDNA with respect to restriction sites and hybridization with the nucleotide probe. Clone pUCADH gamma 21 contained an insertion of 1.5 kilobase pairs (kbp) and encodes 374 amino acid residues compatible with the reported amino acid sequence of the gamma subunit. Clone pUCADH alpha 15L contained an insertion of 2.4 kbp and included nucleotide sequences that encode 374 amino acid residues for another subunit, the alpha subunit. In addition, this clone contained the sequences that encode the COOH-terminal part of the beta subunit at its extended 5' region. The amino acid sequences and coding regions of the cDNAs of the three subunits are very similar (approximately 93-95% identity). A high degree of resemblance is observed also in their 3' noncoding regions. However, distinctive differences exist in the vicinity of the Zn-binding cysteine residue at position 46--i.e., Cys-Gly-Thr in the alpha, Cys-Arg-Thr in the wild-type beta 1, Cys-His-Thr in the Oriental-type beta 2, and Cys-Arg-Ser in the gamma, reflecting the differences in their kinetic properties. Based on the cDNA sequences and the deduced amino acid sequences of the three subunits, their structural and evolutionary relationships are discussed.

Isolation and characterization of the measles virus F1 polypeptide: comparison with other paramyxovirus fusion proteins

Measles virus fusion (F) protein has been isolated by immunoadsorption to a complex of monoclonal antibodies bound to protein A-Sepharose. The 41-kDa F1 component of the fusion protein was obtained pure in high yield by preparative SDS-polyacrylamide gel electrophoresis. The amino acid composition of the F1 chain was determined and the N-terminal sequence was analyzed for 40 residues. The structure determined is largely hydrophobic, with 24 residues of Val, Ile, Leu, Met, Phe, or Ala. Comparison with previously published data on the F1 polypeptide of Sendai virus showed considerable similarity in amino acid composition. Extensive N-terminal sequence homologies with F1 polypeptides of different paramyxoviruses are also noticed, including a nine-residue segment strictly conserved among four F1 polypeptides studied, as well as a weaker but distinct and Gly-rich sequence homology with the influenza A and B virus HA2 polypeptides. The evolutionary conservation of the N-terminal region at the site of cleavage of surface glycoproteins of the two families of myxoviruses highlights its specialized function in membrane fusion.

Structural relationships among class I isozymes of human liver alcohol dehydrogenase

The alpha subunit of human liver alcohol dehydrogenase has been submitted to structural analysis. Together with earlier work on the beta and gamma subunits, the results allow conclusions on the relationship of all known forms of the class I type of the enzyme. Two segments of the alpha subunit were determined; one was also reinvestigated in the beta and gamma subunits. The results establish 11 residue replacements among class I subunits in the segments analyzed and show that the alpha, beta, and gamma protein chains each are structurally distinct in the active site regions, where replacements affect positions influencing coenzyme binding (position 47; Gly in alpha, Arg in beta and gamma) and substrate specificity (position 48; Thr in alpha and beta, Ser in gamma). Residue 128, previously not detected in beta and gamma subunits, corresponds to a position of another isozyme difference (Arg in beta and gamma, Ser in alpha). The many amino acid replacements in alcohol dehydrogenases even at their active sites illustrate that in judgements of enzyme functions absolute importance of single residues should not be overemphasized. Available data suggest that alpha and gamma are the more dissimilar forms within the family of the three class I subunits that have resulted from two gene duplications. The class distinction of alcohol dehydrogenases previously suggested from enzymatic, electrophoretic, and immunological properties therefore also holds true in relation to their structures.

Alcohol dehydrogenases, aldehyde dehydrogenases, and related enzymes

Several new structures have recently been determined for dehydrogenases which are involved in alcohol metabolism. These structures give new insight into catalytic properties, structure-function relationships, and evolutionary connections. They also explain the structural basis for known metabolic deviations. Among alcohol dehydrogenases, the first primary structures for human enzyme forms have been reported (the beta 1, gamma 1, and "atypical" beta-chains). These structures explained functional properties and enzymatic differences, showed separate and parallel events of isozyme divergence, and suggested differential gene activations. Similarly, for aldehyde dehydrogenases, the first cytoplasmic isozyme structures have been reported in man and horse. The data showed positions of functionally important residues, and established clear differences between the mitochondrial and cytoplasmic isozymes of aldehyde dehydrogenase. For sorbitol dehydrogenase, the first complete structure which establishes a relationship with other "long" alcohol dehydrogenases in a scheme exhibiting both structural divergence and functional convergence has also been reported. Finally, glucose dehydrogenase has been structurally linked with sorbitol dehydrogenase, extending the scheme and adding further enzymes to the group of "short" alcohol dehydrogenases.

Sorbitol dehydrogenase. The primary structure of the sheep-liver enzyme

The first primary structure for a sorbitol dehydrogenase has been determined by analysis of the tetrameric enzyme from sheep liver. The [14C]carboxymethylated protein was cleaved with CNBr and proteolytic enzymes. Peptides were purified by several methods, often utilizing exclusion chromatography for pre-fractionation and reverse-phase high-performance liquid chromatography for final purification. Different methods of sequence analysis complemented each other, mainly the manual dimethylaminoazobenzene isothiocyanate method and and the use of liquid-phase sequencer degradations. All eight major CNBr fragments were purified and form the basis of the work. Three minor CNBr fragments derived from an acid cleavage and from a partly resistant Met-Thr bond were also obtained, as well as evidence for a contaminating homologous polypeptide. Most of the tryptic peptides were purified, including all with methionine residues, thus overlapping the CNBr fragments. Combined, all data permit the deduction of a 354-residue amino acid sequence for the polypeptide chain of sorbitol dehydrogenase. The N terminus is acyl-blocked, the C terminus is formed by a proline residue, tryptophan is the least common residue (two, at positions 50 and 301) and there are 10 cysteine residues, including the residue previously shown to be especially reactive (at position 43). Similarities to 'long' alcohol dehydrogenases have functional implications.