Proteinase sequences compared

The sequence of aqualysin Il6) (AQU) is shown compared with those of proteinase Kl7) (PRO), thermitase22 (THE), subtilisin BPN 18 (BPN), and subtilisin El9) (E). Identical amino acids with those of aqualysin I are shown by hyphen (—). Open space is the position where a corresponding amino acid is absent. The numbering above the sequences refers to aqualysin I, and that below the sequences to subtilisins. Asterisks indicate the active-site residues, Asp, His, and Ser. 

Until recently relatively little was known about the molecular basis of lipid hydrolysis. The first amino acid sequence of a triacylglycerol lipase was given by De Caro et al. (1981). As more sequence data became available, it was noted that lipases and esterases share a short consensus sequence, G-X-S-X-G (Boel et al., 1988 Datta et al., 1988 Antonian, 1988 Brenner, 1988). The role of the invariant serine at the center of this sequence was debated (Maraganore and Heinrikson, 1986). Some authors speculated about a lipid recognition site, others compared this pentapeptide to the sequence around the nucleophilic serine in serine proteinases. 

Figure 16.2 shows the results of comparisons of sequences of the aspartic proteinase family of enzymes. It includes pepsins from eukaryotic sources and pro-teinases from retroviruses like human immuno-deficiency virus, HIV. The retroviral proteinases consist of two identical subunits, whereas the pepsins have a single chain with two similar halves, the amino-terminal and the carboxyl-terminal domains, whose structures resemble each other and the subunits of the retroviral proteinases. The sequences of the two domains of the pepsins and the subunits of retroviral proteinases were aligned using COMPARER. Only three residues are identical in all the... 

Fig. 16.2. A section of the alignment of sequences of aspartic proteinases achieved by comparing the three-dimensional structures using COMPARER [14]. HIV human immunodeficiency virus RSV Rous sarcoma virus APE endothiapepsin APP penicillopepsin APR rhizopuspepsin PEP hexagonal porcine pepsin CHY calf chymosin. The last letter refers to the amino (N) or car-boxy (C) terminal domains of the pepsins. The coordinates of the three-dimensional structures were obtained from the PDB databank [24]. The amino acid code is the standard one-letter code (see Appendix C) formatted using the following conventions [7] ...

Although the sequence similarity between the HIV protease and each of the two symmetrical domains of several cellular aspartic proteinases was low, several residues, in addition to the catalytic triad of Asp-Thr/Ser-Gly, critical to the structure and conserved in aspartic proteinase domains and retroviral proteinases, were identified. " There were many uncertainties in the alignment arising fi-om the fact that HTV proteinase had a sequence of only 99 amino acid residues compared to about 160 for a lobe of the pepsin-like aspartic proteinases, but the majority of the deletions could be acconunodated in surface regions. 

To create a set of variants we identified variable amino acid residues by comparing proteinase K with homologous sequeiwes from the serine protease family using standard phylogenetic analysis, structural conq)arisons and principal component analysis. Principal component analysis can be used to reduce the high dimensional complexity of sequence variations by creating new composite dimensions which account for the majority of the difierences within a... 

When comparing the primary structures of a series of related peptide chains, it is common to align the individual chains with gaps to maximize homology. With the fragmentary information available about the amino acid sequences of many aspartate proteinases, it is difficult to make a final recommendation about the numbering of amino acid residues, but the following facts must be considered ... 

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