Summary
Sequences of 47 members of the Zn-containing alcohol dehydrogenase (ADH) family were aligned progressively, and an evolutionary tree with detailed branch order and branch lengths was produced. The alignment shows that only 9 amino acid residues (of 374 in the horse liver ADH sequence) are conserved in this family; these include eight Gly and one Val with structural roles. Three residues that bind the catalytic Zn and modulate its electrostatic environment are conserved in 45 members. Asp 223, which determines specificity for NAD, is found in all but the two NADP-dependent enzymes, which have Gly or Ala. Ser or Thr 48, which makes a hydrogen bond to the substrate, is present in 46 members. The four Cys ligands for the structural zinc are conserved except in ζ-crystallin, the sorbitol dehydrogenases, and two bacterial enzymes. Analysis of the evolutionary tree gives estimates of the times of divergence for different animal ADHs. The human class II (π) and class III (κ) ADHs probably diverged about 630 million years ago, and the newly identified human ADH6 appeared about 520 million years ago, implying that these classes of enzymes may exist or have existed in all vertebrates. The human class I ADH isoenzymes (α, β, and γ) diverged about 80 million years ago, suggesting that these isoenzymes may exist or have existed in all primates. Analysis of branch lengths shows that these plant ADHs are more conserved than the animal ones and that class III ADHs are more conserved than class I ADHs. The rate of acceptance of point mutations (PAM units) shows that selection pressure has existed for ADHs, implying that these enzymes play definite metabolic roles.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Aronson BD, Somerville RL (1989) The primary structure of E. coli l-threonine dehydrogenase. J Biol Chem 264:5226–5232
Bennetzen JL, Hall BD (1982) The primary structure of the Saccharomyces cerevisiae gene for alcohol dehydrogenase I. J Biol Chem 257:3018–3025
Borrás T, Persson B, Jörnvall H (1989) Eye lens ζ crystallin relationships to the family of “long-chain” alcohol/polyol dehydrogenases. Protein trimming and conservation of stable parts. Biochemistry 28:6133–6139
Brändén CI, Jörnvall H, Eklund H, Furugren B (1975) Alcohol dehydrogenases. In: Boyer PD (ed) The enzymes, ed 3, vol XI. Academic Press, New York, pp 104–190
Carroll RL (1988) Vertebrate paleontology evolution. Freeman, New York
Cederlund E, Peralba JM, Pares X, Jörnvall H (1991) Amphibian alcohol dehydrogenase, the major frog liver enzyme. Relationships to other forms and assessment of an early gene duplication separating vertebrate class I and class III alcohol dehydrogenases. Biochemistry 30:2811–2816
Chang C, Meyerowitz EM (1986) Molecular cloning and DNA sequence of the Arabidopsis thaliana alcohol dehydrogenase gene. Proc Natl Acad Sci USA 83:1408–1412
Chen CS, Yoshida A (1991) Enzymatic properties of the protein encoded by newly cloned human alcohol dehydrogenase ADH6 gene. Biochem Biophys Res Commun 181:743–747
Crabb DW, Edenberg HJ (1987) Complete amino acid sequence of rat liver alcohol dehydrogenase deduced from the cDNA se1uence. Gene 48:287–290
Creaser EH, Murali C, Britt KA (1990) Protein engineering of yeast alcohol dehydrogenases; effects of amino acid changes at positions 93 and 48 of yeast ADH1. Protein Eng 3:523–526
Dayhoff MO (1976) Survey of new data and computer methods of analysis. In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5, suppl 2. National Biomedical Research Foundation, Washington DC, pp 1–8
Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model for evolutionary change. In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5, suppl 3. National Biomedical Research Foundation, Washington DC, pp 345–358
Dennis ES, Sachs MM, Gerlach WL, Finnegan ET, Peacock WJ (1985) Molecular analysis of the alcohol dehydrogenase 2 (Adh2) gene of maize. Nucleic Acids Res 13:727–743
Devereux J, Haeberli P, Smithies O (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387–395
Doolittle RF, Feng DF (1990) Nearest neighbor procedure for relating progressively aligned amino acid sequences. Methods Enzymol 183:659–669
Drum DE, Li TK, Vallee BL (1969) Considerations in evaluating the zinc content of horse liver alcohol dehydrogenase preparations. Biochemistry 8:3783–3797
Edenberg HJ, Zhang K, Fong K, Bosron WF, Li TK (1985) Cloning and sequencing of cDNA encoding the complete mouse liver alcohol dehydrogenase. Proc Natl Acad Sci USA 82: 2262–2266
Edenberg HJ, Brown CJ, Carr LG, Ho WH, Hur MW (1991) Alcohol dehydrogenase gene expression and cloning of the mouse ξ-like alcohol dehydrogenase. Adv Exp Med Biol 284: 253–262
Ehrig T, Hurley TD, Edenberg HJ, Bosron WF (1991) General base catalysis in a glutamine for histidine mutant at position 51 of human liver alcohol dehydrogenase. Biochemistry 30: 1062–1068
Eklund H, Branden CI (1987) Alcohol dehydrogenase. In: Jurnak FA, McPherson A (eds) Biological macromolecules and assemblies, vol 3. Active sites of enzymes. John Wiley, New York, pp 73–142
Eklund H, Plapp BV, Samama JP, Brändén CI (1982) Binding of substrate in a ternary complex of horse liver alcohol dehydrogenase. J Biol Chem 257:14349–14358
Eklund H, Samama JP, Jones TA (1984) Crystallographic investigations of nicotinamide adenine dinucleotide binding to horse liver alcohol dehydrogenase. Biochemistry 23:5982–5996
Eklund H, Horjales E, Jörnvall H, Brändén CI, Jeffery J (1985) Molecular aspects of functional differences between alcohol and sorbitol dehydrogenases. Biochemistry 24:8005–8012
Eklund H, Horjales E, Vallee BL, Jörnvall H (1987) Computer-graphics interpretations of residue exchanges between the α, β and γ subunits of human liver alcohol dehydrogenase class I isozymes. Eur J Biochem 167:185–193
Eklund H, Müller-Wille P, Horjales E, Futer O, Holmquist B, Vallee BL, Höög JO, Kaiser R, Jörnvall H (1990) Comparison of three classes of human liver alcohol dehydrogenase. Eur J Biochem 193:303–310
Ellison NW (1989) EMBL Data Library, S06200
Estonius M, Karlsson C, Fox EA, Höög JO, Holmquist B, Vallee BL, Davidson WS, Jörnvall H (1990) Avian alcohol dehydrogenase: the chicken liver enzyme. Eur J Biochem 194: 593–602
Fan F, Lorenzen JA, Plapp BV (1991) An aspartate residue in yeast alcohol dehydrogenase I determines the specificity for coenzyme. Biochemistry 30:6397–6401
Feng DF, Doolittle RF (1990) Progressive alignment and phylogenetic tree construction of protein sequences. Methods Enzymol 183:375–389
Ganzhorn AJ, Plapp BV (1988) Carboxyl groups near the active site zinc contribute to catalysis in yeast alcohol dehydrogenase. J Biol Chem 263:5446–5454
Good AG, Pelchen LE, Crosby WL (1988) Nucleotide sequence of a complete barley alcohol dehydrogenase I cDNA. Nucleic Acids Res 16:7182
Gwynne DI, Buxton FP, Sibley S, Davies RW, Lockington RA, Scazzocchio C, Sealy-Lewis HM (1987) Comparison of the cis-acting control regions of two coordinately controlled genes involved in ethanol utilization in Aspergillus nidulans. Gene 51:205–216
Ha BD, Buffardd D, Breda C, Esnault R (1989) EMBL Data Library, S06693
Holmes MA, Matthews BW (1981) Binding of hydroxamic acid inhibitors to crystalline thermolysin suggests a pentacoordinate zinc intermediate in catalysis. Biochemistry 20:6912–6920
Holmes RS, Courtney YR, VandeBerg JL (1986) Alcohol dehydrogenase in baboons: tissue distribution, catalytic properties, and variant phenotypes in liver, kidney, stomach, and testis. Alcoholism 10:623–630
Holmes RS, VandeBerg JL (1986) Ocular NAD-dependent alcohol dehydrogenase and aldehyde dehydrogenase in the baboon. Exp Eye Res 43:383–396
Höög JO, Hedén LO, Larsson K, Jörnvall H, von Bahr-Lindström H (1986) The γ1 and γ2 subunits of human liver alcohol deydrogenase. cDNA structures, two amino acid replacements, and compatibility with changes in the enzymatic properties. Eur J Biochem 159:215–218
Höög JO, von Bahr-Lindström H, Heden LO, Holmquist B, Larsson K, Hempel J, Vallee BL, Jörnvall H (1987) Structure of the class II enzyme of human liver alcohol dehydrogenase: combined cDNA and protein sequence determination of the π subunit. Biochemistry 26:1926–1932
Hurley TD, Bosron WF, Hamilton JA, Amzel LM (1991) Structure of human β1β1 alcohol dehydrogenase: catalytic effects of non-active-site substitutions. Proc Natl Acad Sci USA 88: 8149–8153
Ikuta T, Fujiyoshi T, Kurachi K, Yoshida A (1985) Molecular cloning of a full-length cDNA for human alcohol dehydrogenase. Proc Natl Acad Sci USA 82:2703–2707
Ikuta T, Szeto S, Yoshida A (1986) Three human alcohol dehydrogenase subunits: cDNA structure and molecular evolutionary divergence. Proc Natl Acad Sci USA 83:634–638
Jeffery J, Chester J, Mills C, Sadler PJ, Jörnvall H (1984) Sorbitol dehydrogenase is a zinc enzyme. EMBO J 3:357–360
Jendrossek D, Steinbüchel A, Schlegel HG (1988) Alcohol dehydrogenase gene from Alcaligenes eutrophus: subcloning, heterologous expression in E. coli, sequencing, and location of Tn5 insertions. J Bacteriol 170:5248–5256
Johnson MS, Sutcliffe MJ, Blundell TL (1990) Molecular anatomy: phyletic relationships derived from three-dimensional structures of proteins. J Mol Evol 30:43–59
Jörnvall H (1970) Horse liver alcohol dehydrogenase. Eur J Biochem 16:25–40
Jörnvall H, Persson M, Jeffery J (1981) Alcohol and polyol dehydrogenases are both divided into two protein types, and structural properties cross-relate the different enzyme activities within each type. Proc Natl Acad Sci USA 78:4226–4230
Jörnvall H, Persson B, Jeffery J (1987) Characteristics of alcohol/polyol dehydrogenases. Eur J Biochem 167:195–201
Julià P, Parés X, Jörnvall H (1988) Rat liver alcohol dehydrogenase of class III. Eur J Biochem 172:73–83
Kadowaki KI, Matsuoka M, Murai N, Harada K (1988) Induction of two alcohol dehydrogenase polypeptides in rice roots during anaerobiosis. Plant Science 54:29–36
Kaiser R, Holmquist B, Hempel J, Vallee BL, Jörnvall H (1988) Class III human liver alcohol dehydrogenase: a novel structural type equidistantly related to the class I and class II enzymes. Biochemistry 27:1132–1140
Kaiser R, Holmquist B, Vallee BL, Jörnvall H (1989) Characteristics of mammalian class III alcohol dehydrogenases, an enzyme less variable than the traditional liver enzyme of class I. Biochemistry 28:8432–8438
Kaiser R, Nussrallah B, Dam R, Wagner FW, Jörnvall H (1990) Avian alcohol dehydrogenase. Characterization of the quail enzyme, functional interpretations, and relationships to the different classes of mammalian alcohol dehydrogenase. Biochemistry 29:8365–8371
Karlsson C, Jörnvall H, Höög JO (1991) Sorbitol dehydrogenase: cDNA coding for the rat enzyme. Eur J Biochem 198: 761–765
Kassam JP, Tang BK, Kadar D, Kalow W (1989) In vitro studies of human liver ADH variants using a variety of substrates. Drug Metab Dispos 17:567–573
Keshav KF, Yomano LP, An H, Ingram LO (1990) Cloning of the Zymomonas mobilis structural gene encoding alcohol dehydrogenase I (adhA): sequence comparison and expression in E. coli. J Bacteriol 172:2491–2497
Kim EE, Wyckoff HW (1991) Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis. J Mol Biol 218:449–464
Koivusalo M, Uotila L (1991) Glutathione-dependent formaldehyde dehydrogenase: evidence for the identity with class III alcohol dehydrogenase. Adv Exp Med Biol 284:241–251
Li TK, Bosron WF, Dafeldecker WP, Lange LG, Vallee BL (1977) Isolation of π-alcohol dehydrogenase of human liver: is it a determinant of alcoholism? Proc Natl Acad Sci USA 74:4378–4381
Light DR, Dennis MS, Forsythe IJ, Liu CC, Green DW, Kratzer DA, Plapp BV (1992) GenBank, M81807
Llewellyn DJ, Finnegan EJ, Ellis JG, Dennis ES, Peacock WJ (1987) Structure and expression of an alcohol dehydrogenase 1 gene from Pisum sativum. J Mol Biol 195:115–123
Matthews BW, Weaver LH, Kester WR (1974) The conformation of thermolysin. J Biol Chem 249:8030–8044
Matton DP, Brisson N (1990) Nucleotide sequence of two potato alcohol dehydrogenase cDNAs. Nucleic Acids Res 18: 3070
McKnight GL, Kato H, Upshall A, Parker MD, Saari G, O'Hara PJ (1985) Identification and molecular analysis of a third Aspergillus nidulans alcohol dehydrogenase gene. EMBO J 4: 2093–2099
Mitchell LE, Dennis ES, Peacock WJ (1989) Molecular analysis of an alcohol dehydrogenase gene from chromosome 1 of wheat. Genome 32:349–358
Monaco HL, Crawford JL, Lipscomb WN (1978) Three-dimensional structures of aspartate carbamoyltransferase from E. coli and of its complex with cytidine triphosphate. Proc Natl Acad Sci USA 75:5276–5280
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443–453
Ohlsson I, Nordström B, Brändén CI (1974) Structural and functional similarities within the coenzyme binding domains of dehydrogenases. J Mol Biol 89:339–354
Parés X, Vallee BL (1981) New human liver alcohol dehydrogenase forms with unique kinetic characteristics. Biochem Biophys Res Commun 98:122–130
Park DH (1991) PhD Thesis, Structure and function of isoenzymes of horse liver alcohol dehydrogenase. The University of Iowa, Iowa City
Park DH, Plapp BV (1991) Isoenzymes of horse liver alcohol dehydrogenase active on ethanol and steroids. J Biol Chem 266:13296–13302
Peretz M, Burstein Y (1989) Amino acid sequence of alcohol dehydrogenase from the thermophilic bacteria Thermoanaerobium brockii. Biochemistry 28:6549–6555
Plapp BV, Ganzhorn AJ, Gould RM, Green DW, Jacobi T, Warth E, Kratzer DA (1991) Catalysis by yeast alcohol dehydrogenase. Adv Exp Med Biol 284:241–251
Rao PV, Krishna CM, Zigler JS (1992) Identification and characterization of the enzymatic activity of ζ-crystallin from guinea pig lens. J Biol Chem 267:96–102
Rees DC, Lewis M, Honzatko RB, Lipscomb WN, Hardman KD (1981) Zinc enviroment and cis peptide bonds in carboxy-peptidase A at 1.75 Å resolution. Proc Natl Acad Sci USA 78:3408–3412
Ricard B, Mocquot B, Fournier A, Delseny M, Pradet A (1986) Expression of alcohol dehydrogenase in rice embryos under anoxia. Plant Mot Biol 7:321–329
Russell DW, Smith M, Williamson VM, Young ET (1983) Nucleotide sequence of the yeast alcohol dehydrogenase II gene. J Biol Chem 258:2674–2682
Russell PR, Hall BD (1983) The primary structure of the alcohol dehydrogenase gene from the fission yeast Schizosaccharomyces pombe. J Biol Chem 258:143–149
Saliola, M, Shuster JR, Falcone C (1990) The alcohol dehydrogenase system in the yeast, Kluyveromyces lactis. Yeast 6:193–204
Smith M, Hopkinson DA, Harris H (1971) Development changes and polymorphism in human alcohol dehydrogenase. Ann Hum Genet 34:251–271
Trezise AEO, Godfrey EA, Holmes RS, Beacham IR (1989) Cloning and sequencing of cDNA encoding baboon liver alcohol dehydrogenase: evidence for a common ancestral lineage with the human alcohol dehydrogenase β subunit for class I alcohol dehydrogenase gene duplications predating primate radiation. Proc Natl Acad Sci USA 86:5454–5458
Trick M, Dennis ES, Edwards KJR, Peacock WJ (1988) Molecular analysis of the alcohol dehydrogenase gene family of barley. Plant Mot Biol 11:147–160
Vallee BL, Auld DS (1990) Active-site zinc ligands and activated H2O of zinc enzymes. Proc Natl Acad Sci USA 87:220–224
Vallee BL, Bazzone TJ (1983) Isozymes of human liver alcohol dehydrogenase. In: Rattazzi MC, Scandalios JG, Witt GS (eds) Current topics in biological medical research, vol 8. Liss, New York, pp 219–244
von Bahr-Lindström H, Höög JO, Hedén LO, Kaiser R, Fleetwood L, Larsson K, Lake M, Holmquist B, Holmgren A, Hempel J, Vallee BL, Jörnvall H (1986) cDNA and protein structure for the α subunit of human liver alcohol dehydrogenase. Biochemistry 25:2465–2470
Wolyn DJ, Jelenkovic G (1990) Nucleotide sequence of an alcohol dehydrogenase gene in octoploid strawberry. Plant Mot Biol 14:855–857
Xie Y, Wu R (1989) Rice alcohol dehydrogenase genes: anaerobic induction, organ specific expression and characterization of cDNA clones. Plant Mot Biol 13:53–68
Xie Y, Wu R (1990) Molecular analysis of an alcohol dehydrogenase-encoding genomic clone (adh2) from rice. Gene 87:185–191
Yasunami M, Chen CS, Yoshida A (1990) Multiplication of the class I alcohol dehydrogenase locus in mammalian evolution. Biochem Genet 28:591–599
Yasunami M, Chen CS, Yoshida A (1991) A human alcohol dehydrogenase gene (ADH6) encoding an additional class of isozyme. Proc Natl Acad Sci USA 88:7610–7614
Yokoyama S, Yokoyama R, Kinlaw C, Harry DE (1990) Molecular evolution of the zinc-containing long-chain alcohol dehydrogenase genes. Mot Biol Evol 7:143–154
Young ET, Pilgrim D (1985) Isolation and DNA sequence of ADH3, a nuclear gene encoding the mitochondrial isozyme of alcohol dehydrogenase in Saccharomyces cerevisiae. Mot Cell Biol 5:3024–3034
Author information
Authors and Affiliations
Additional information
Offprint requests to: B.V. Plapp
Rights and permissions
About this article
Cite this article
Sun, HW., Plapp, B.V. Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family. J Mol Evol 34, 522–535 (1992). https://doi.org/10.1007/BF00160465
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF00160465