Partial Similarities Between Yeast and Liver Alcohol Dehydrogenases

1992

Protein Science

Self Cite

Analysis of tomato pectinesterase by carboxymethylation, with and without reduction, shows that the enzyme has two intrachain disulfide bridges. Analysis of fragments obtained from the native enzyme after digestion with pepsin identified bridges connecting . The locations of disulfide bridges in tomato pectinesterase are not identical to those in three distantly related pectinesterases (18-33% residue identities) from microorganisms. However, one half-Cys (i.e., position is conserved in all four enzymes. Sequence comparisons of the overall structures suggest a special importance for three short segments of the entire protein. One segment is at the N-terminal part of the tomato pectinesterase, another in the C-terminal portion near the distal end of the second disulfide loop, and the third segment is located in the central part between the two disulfide bridges. The latter segment, encompassing only 40 residues of the entire protein, appears to highlight a functional site in a midchain segment.Keywords: active site segments; disulfides; pectinesterase; structural variation Pectic enzymes are degradative enzymes, involving both deesterifying hydrolases, deglycosidating hydrolases, and deglycosidating lyases. Together, they control breakdown of the heteropolysaccharide pectin in plants (Rombouts & Pilnik, 1980) and regulate both physiological processes and pathogenic processes such as infection by phytopathogenic microorganisms (Collmer & Keen, 1986). To date, four different types of pectinesterase have been determined in primary structure, the pectinesterase from tomato (Ray et al., 1988;MarkoviE & Jornvall, 1990), Aspergillus niger (Khanh et al., 1990), Erwinia chrysanthemi (Plastow, 1988), and Pseudomonas solanacearum (Spok et al., 1991). These four enzymes are distantly related, exhibiting a low degree of sequence similarity, with residue identities at the 18-33% level (disregarding an elongated N-terminal overshooting end of the Pseudomonas enzyme). Attempts at chemical modifications have shown the presence of reactive tyrosine residues (MarkoviE, 1983), and overall comparisons suggest relationships within both this family of pectinesterases, and that -.Correspondence to: Hans Jornvall, Department of Chemistry I, Karolinska Institutet, S-104 01 Stockholm, Sweden. of polygalacturonases, which are also pectic degradative enzymes (Plastow, 1988;Hinton et al., 1990). Furthermore, pectinesterase homologs exist and help to define elements of structural interest (Albani et al., 1991). However, information on functional mechanisms, active site locations, and overall organization of the proteins is limited.We have now determined the arrangement of disulfide bridges in the tomato enzyme. Two intrachain bridges were detected. Comparisons of their locations with those of cysteine/half-cystine positions in other pectinesterases reveal fairly large variations. We clearly show regions of conserved primary structure in all of these pectinesterases that suggest a functional role for a mid-chain segment. Results Pr...

Section: Discussionsupporting

confidence: 71%

Disulfide bridges in tomato pectinesterase: Variations from pectinesterases of other species; conservation of possible active site segments

Markovič

1992

Protein Science

Self Cite

“…Early on, these two enzymes were considered quite separate in the ‘bible’ of that time (‘The Enzymes’, 2 nd edition, [ 31 ]) and had different cysteine residues reactive towards labelling reagents [ 32 , 33 ], but were given the same Enzyme Commission number (EC 1.1.1.1) when that system was introduced. Later on, a clear relationship between liver and yeast ADHs was established [ 34 ], the common yeast ADH characterised [ 35 ] and subsequently many additional forms. Overall, most of the yeast ADHs, versus the liver enzymes, lack an internal segment, affecting subunit interactions [ 36 ] and hence the quaternary structure.…”

Section: Highly Widespread Mdr Familiesmentioning

confidence: 99%

Medium- and short-chain dehydrogenase/reductase gene and protein families

Persson

Hedlund

2008

Cell. Mol. Life Sci.

162

112

Abstract. The MDR superfamily with~350-residue subunits contains the classical liver alcohol dehydrogenase (ADH), quinone reductase, leukotriene B4 dehydrogenase and many more forms. ADH is a dimeric zinc metalloprotein and occurs as five different classes in humans, resulting from gene duplications during vertebrate evolution, the first one traced to~500 MYA (million years ago) from an ancestral formaldehyde dehydrogenase line. Like many duplications at that time, it correlates with enzymogenesis of new activities, contributing to conditions for emergence of vertebrate land life from osseous fish. The speed of changes correlates with function, as do differential evolutionary patterns in separate segments. Subsequent recognitions now define at least 40 human MDR members in the Uniprot database (correA C H T U N G T R E N N U N G sponding to 25 genes when excluding close homologues), and in all species at least 10 888 entries. Overall, variability is large, but like for many dehydrogenases, subdivided into constant and variable forms, corresponding to household and emerging enzyme activities, respectively. This review covers basic facts and describes eight large MDR families and nine smaller families. Combined, they have specific substrates in metabolic pathways, some with wide substrate specificity, and several with little known functions.

“…For steric reasons this residue is over-represented when similar but distantly related proteins are compared [41,10] and for many positions in the horse liver enzyme no other residue than glycine is compatible with the space available [36]. In a large part of the first half of the coenzyme-binding domain (total positions 196-266 with two of the central 8-pleated sheet stretches, marked A and B [36] in Fig.…”

Section: Structure-function Relationshipsmentioning

confidence: 99%

Differences between Alcohol Dehydeogenases

European Journal of Biochemistry

1977

110

Comparisons of the primary structures of yeast and horse liver alcohol dehydrogenases reveal that the enzymes are homologous but distantly related. The overall positional identity is 25 between common regions, and several deletions/insertions occur in either enzyme, the longest apparently corresponding to 21 residues, showing that the different subunit sizes are largely explained by internal differences.Variabilities in the structural similarities can be coupled with functional requirements but not directly with whole domains in the previously known tertiary structure of the horse protein. The two most similar regions of the enzymes affect active-site segments and the two most dissimilar regions seem to affect a loop structure without known function, and a segment participating in subunit interactions. The dissimilarities may probably be correlated with changes in zinc-binding properties and quaternary structures.The extra region corresponding to the large internal chain-length difference shows an apparent coincidence in sequence to a following segment of the horse enzyme, and additional elements of internal coincidences, or superficial similarities with other dehydrogenases, are noticed. These characteristics are not fully distinguishable from chance distributions but in view of the extensive species variations in alcohol dehydrogenases some evolutionary considerations may not be excluded, in which case a model relating all regions of these and associated enzymes to a common ancestor is shown to be compatible with all known observations.