Amino acid sequence comparisons

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Figure 1. An unrooted phylogenetic tree of the myosins based on the amino acid sequence comparison of their head domains demonstrating the division of the myosin superfamily into nine classes. The lengths of the branches are proportional to the percent of amino acid sequence divergence and a calibration bar for 5% sequence divergence is shovk n. The different classes of myosins have been numbered using Roman numerals in rough order of their discovery and hypothetical models of the different myosin structures are shown. Question marks indicate either hypothetical or unknown structural features, and only a fraction of the known myosins are shown. (Taken, in modified form, from Cheney et al., 1993).

Figure 2. Schematic amino acid sequence comparison between the two...

Gorbalenya, A.E. and Koonin, E.V. (1993) Helicases amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3, 419-429. 

FIGURE 3-33 Evolutionary tree derived from amino acid sequence comparisons. A bacterial evolutionary tree, based on the sequence divergence observed in the GroEL family of proteins. Also included in this tree (lower right) are the chioropiasts (chi.) of some nonbacteriai species. 

Whereas amino acid sequence comparisons suggested that the homeodomain would contain a helix-turn-helix motif, the 60-residue homeodomain forms a stable structure that can bind to DNA as a monomer. The recognition helix in the homeodomain is longer and makes more contacts with the DNA core than the recognition helices from bacterial regulatory proteins (fig. 31.18). 

Urease (urea amidohydrolase) is an enzyme first identified over a hundred years ago in bacterial extracts [22], The presence of urease is a virulence factor for some pathogenic bacteria [23,24], It is now known to occur also in plants, fungi, and invertebrates (see [24,25] for reviews). Urease from jack bean was the first enzyme to be crystallized, in 1926. Almost 50 years later its metal content was reexamined and it was found to contain two atoms of nickel per subunit [26]. Finally in 1995 the crystal structure of the enzyme from the enteric bacterium Klebsiella aerogenes was determined [27], Amino-acid sequence comparisons predict that the structures of the plant and bacterial enzymes are similar, although with different subunit arrangements. 

Amino acid sequence comparisons with known reductases will continue to play a major role in identifying enzymes in baker s yeast and other species. Several groups have identified key sequence patterns in different reductase superfamilies that allow one to determine whether a protein sequence is consistent with a role in carbonyl reductions [43-45,64,80], While several of these motifs have been discussed above, a complete collection has been assembled in Table 2, which also indicates the level of conservation of these motifs among the yeast open reading frames discussed previously. 

Amino acid sequence comparison of a-glucan phosphorylases. H, the potato type-H isozyme L, the potato type-L isozyme and R, rabbit muscle phosphotylase.791 The type-H isozyme sequence is used as the reference sequence only the amino acid residues that are nonidentical in the type-L isozyme and rabbit muscle enzyme are indicated. (From Biol. Chem., 266 (28), 18453 (1991)). 

Fig-i Structural considerations about drug binding in the Kvl.5 channel pore. Amino acid sequence comparison of alpha subunit sequences from human Kvl.1-1.6 and Kv2.1, Kvll.l (hERG), Kv7.1 (KvLQTl). Symbols indicate complete amino acid conservation ( ), conservative substitution among all aligned sequences ( ), and critical substitution in a generally conserved position (.)... 

Fig. 3.3 Dendrogram of evolutionary relationships between 87 basidiomycete (and two reference ascomycete) peroxidases, including structural-functional classification based on Ruiz-Duenas et al. [10] (GeneBank and P. ostreatus genome references in parentheses). Amino acid sequence comparisons as Poisson distances and clustering based on UPGMA and pair-wise deletion option of MEGA4 [43]...

Amino acid sequence comparison of the different Ty s shows that they are structurally related. The sequence identity is 24% between bacterial and fungal Ty and 26% between mouse and N. crassa Ty. A comparison of all three types of Ty (bacterial, ftmgal, and mammalian) reveals a sequence identity of only 8.7%. 

Fig. 1 Primary amino acid sequence comparison between five members of the human somatostatin receptor family. The amino acid sequences are aligned, using the single-letter amino acid code. Gaps introduced in the sequences to optimize the alignments are represented with dashes (-). The boxes indicate amino acids that are identical in all five receptor subtypes. The highest level of homology occurs within the seven canonical transmembrane domains of the human SST receptors (indicated above the sequences) and these domains have been derived by a combination of hydropathy analysis and comparison with the transmembrane domains of the other G-protein coupled receptors. The high level of homology among the members of the SST receptor family in the seven membrane spanning domains is shared by other G-protein coupled receptors that are coupled to inhibition of adenylyl cyclase.

Feng, D. F., Johnson, M. S., and Doolittle, R. F. (1985) Aligning amino acid sequences comparison of commonly used methods. J. Mol. Evol. 212, 112-125. 

The central copper ion of the auracyanins is probably coordinated by two histidines, one cysteine, and a methionine residue. The auracyanins are unique among the small blue proteins in that they possess a methionine and a glutamine residue (see phytocyanins) which both could act as the fourth ligand coordinating the central copper ion. This copper center is surrounded by a hydro-phobic environment similar to that of the other small blue proteins [68]. Amino acid sequence comparisons place auracyanin in a phylogenetic tree at approximately equal distances from azurin and plastocyanin [68,92]. 

Amino acid sequence comparisons of the other type 2 copper proteins with various copper and non-copper proteins did not detect any significant phylogenetic relationship. 

Evolutionary relationships can be assessed by comparison of three-dimensional structures. Indeed, structural comparisons can be used to trace divergent evolution over longer time spans than is possible by amino acid sequence comparisons. The considerable similarity of VP1, VP2 and VP3 structures to those of the plant viruses leaves little doubt as to their divergence from a common ancestor. 

Table IV also lists the structure analyses of three bacterial cytochromes. Logically these should be delayed to the second half of the chapter, but the results have had such an important influence on thinking about oxidation-reduction mechanisms that their discussion here is mandatory. A key structure study from an evolutionary standpoint was that of R. rvhrum by Salemme, Kraut, and colleagues at the University of California, San Diego (30,31). That study established in one stroke that the eukaryotic cytochrome fold also extended to a bacterial cytochrome and included the cytochromes of photosynthesis as well as respiration. The fact that this structural homology had been predicted on the basis of amino acid sequence comparisons (32) did not lessen the excitement of seeing direct confirmation from the molecular model. Only one of three possible conclusions can be drawn ...

As shown in Scheme 1, NHase catalyzes the conversion of nitriles to amides 4), The active site contains either a non-corrin cobalt(III) or non-heme iron(III). Amino acid sequence comparisons have shown that the primary coordination sphere is conserved regardless of the identity of the metal center and consists of a -C-S-L-C-S-C- motif (5). EPR studies on Fe-NHase revealed the iron center maintains a low-spin Fe(III) state throughout the catalytic cycle, and that the iron center has a variable coordination site for substrate interaction (6). These findings are consistent with the hypothesis that the enzyme functions solely as a hydrolytic (i.e., redox-inactive) catalyst. Incubation of the enzyme with nitric oxide in the dark inactivates the enzyme. Exposure to light was found to reinstate activity with concomitant loss of NO, thus revealing a novel photo-regulatory mechanism (7-70). 

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