Similar with different amino acid sequences

Many enzymes exist within a cell as two or more isoenzymes, enzymes that catalyze the same chemical reaction and have similar substrate specificities. They are not isomers but are distinctly different proteins which are usually encoded by different genes.22 23 An example is provided by aspartate aminotransferase (Fig. 2-6) which occurs in eukaryotes as a pair of cytosolic and mitochondrial isoenzymes with different amino acid sequences and different isoelectric points. Although these isoenzymes share less than 50% sequence identity, their internal structures are nearly identical.24-27 The two isoenzymes, which also share structural homology with that of E. coli,28 may have evolved separately in the cytosol and mitochondria, respectively, from an ancient common precursor. Tire differences between them are concentrated on the external surface and may be important to as yet unknown interactions with other protein molecules. 

Domains are formed by different combinations of secondary structure elements and motifs. The a helices and p strands of the motifs are adjacent to each other in the three-dimensional structure and connected by loop regions. Sequentially adjacent motifs, or motifs that are formed from consecutive regions of the primary structure of a polypeptide chain, are usually close together in the three-dimensional structure (Figure 2.20). Thus to a first approximation a polypeptide chain can be considered as a sequential arrangement of these simple motifs. The number of such combinations found in proteins is limited, and some combinations seem to be structurally favored. Thus similar domain structures frequently occur in different proteins with different functions and with completely different amino acid sequences. 

We have described a general relationship between structure and function for the a/p-barrel structures. They all have the active site at the same position with respect to their common structure in spite of having different functions as well as different amino acid sequences. We can now ask if similar relationships also occur for the open a/p-sheet structures in spite of their much greater variation in structure. Can the position of the active sites be predicted from the structures of many open-sheet a/p proteins ... 

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

How does one go about finding all of the relevant proteins in a database once it has been decided to carry out an analysis of an entire protein family The simplest approach is to use similarity search software such as SSEARCH or FASTA (Smith and Waterman, 1981 Pearson and Lipman, 1988) or BLAST (Altschul et al, 1997) with the amino acid sequences of one or two well-known members of the family as queries. The problem is initially the same as that of identifying all proteins that are homologous to a family of proteins, although with some important practical differ-... 

First, as we have already noted, proteins with different functions always have different amino acid sequences. Second, thousands of human genetic diseases have been traced to the production of defective proteins. Perhaps one-third of these proteins are defective because of a single change in their amino acid sequence hence, if the primary structure is altered, the function of the protein may also be changed. Finally, on comparing functionally similar proteins from different species, we find that these proteins often have similar amino acid sequences. An extreme case is ubiquitin, a 76-residue protein involved in regulating the degradation of other proteins. The amino acid sequence of ubiquitin is identical in species as disparate as fruit flies and humans. 

Even though the roles of IF-2, EF-Tu, EF-G, and RF-3 in protein synthesis are quite different, all four of these proteins share a domain with significant amino acid sequence similarity. Suggest a role for this conserved domain. 

The comparison of protein folds has proved to be difficult the three-dimensional structures are frequently complicated, and quite significant differences can exist between structures that are, on the basis of sequence similarity, clearly related in evolutionary terms. On the other hand structures may sometimes resemble each other very closely, but fail to display any sequence similarity the classic example of this is the parallel beta barrel structure which has now been found in more than twenty proteins with no amino-acid sequence homology [35], In these cases the interpretation of the meaning of a similarity can be less than straightforward it may indicate that the proteins are evolutionary related ( divergent evolution ), that they are unrelated but have evolved similar structures because they carry out similar functions ( convergent evolution ) or the common structure may simply be a particularly stable one that is adopted by a large number of proteins. In addition to three similarities between complete protein folds, there may also be partial similarities. 

COX-1 and COX-2 are of similar molecular mass (approximately 70 and 72 kDa respectively), with 65% amino acid sequence homology and near-identical catalytic sites. The most significant difference between the isoenzymes, which allows for selective inhibition, is the substitution of isoleucine at position 523 in COX-1 with valine in COX-2. The relatively smaller Val523 residue in COX-2 allows access to a hydrophobic side-pocket in the enzyme (which Ile523 sterically hinders). Drugs, such as the coxibs, bind to this alternative site and are considered to be selective inhibitors of COX-2. 

Transfer RNA molecules are the adaptors that associate an amino acid with its correct base sequence. Transfer RNA molecules are structurally similar to one another each adopts a three-dimensional cloverleaf pattern of base-paired groups (Figure 2,10). Subtle differences in structure enable the protein-synthesis machinery to distinguish transfer RNA molecules with different amino acid specificities. 

It was recognized early that DNA topoisomerases are interesting enzymes from an evolutionary point of view, since they catalyze different reactions in eukaryotes and in eubacteria, with probably important consequences on chromosome structure and on relationships between DNA topology and gene expression [67], In eukaryotes, the major type I DNA topoisomerase relaxes either positive or negative supertums, whereas the two eubacterial type I DNA topoisomerases that have been described (protein u and E. coli DNA topoisomerase III) relax only negative supertums (Fig. 6). In addition, the eukaryotic type I DNA topoisomerase is transiently linked to the 3 end of the DNA break, whereas the two eubacterial type I DNA topoisomerases are covalently linked to the 5 end. These (3 ) and (5 ) type I DNA topoisomerases are not only mechanistically but also phylogenetically umelated, as indicated by the complete absence of similarity in their amino-acid sequences. 

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