Homology sequence

The structural genes of seventeen E-IIs and E-IIIs have been sequenced. In addition to the 15 listed in Table 1 of [5], the sequences of of R. capsulatus [6] and E- 

IIA ° with 61% sequence similarity and a moderately hydrophobic IIM and IIM with 63% sequence similarity. 

Sequence data, in combination with functional studies, reveal several classes of E-IIs as shown in Fig. 3. These classes will most likely change and expand as future studies define additional domains with new functions. We introduce it here, only for the sake of our own convenience, in this chapter. The first class is represented by E. coli II . This protein is unique in that, as yet, it is the only representative of its class. It consists only of a single hydrophobic peptide with no hydrophilic domain attached at either end [7,9]. 

The second class, represented by E. coli 11°, consists of a hydrophobic domain of approximately 360 residues followed by hydrophilic domain of approximately 100 residues [10], Other representatives of this class are E. coli 11° [11], S. aureus 11 [12], E. coli [13,14] B. subtilis 11 [15] and 11 encoded by the plasmid pUR400 [16]. 

The third class, represented by E. coli consists again of a single hydrophobic domain of approximately 360 residues but with two covalently attached hydrophilic domains, equal, together, in size to the hydrophobic domain [17], The A domain is proposed to function as a covalently attached E-III. Other representatives of this class include B. subtilis II° [18,19], 5. mutans 11 [20], E. coli II [21,22] and [23,24], 

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Prolactin-Like Proteins. A number of prolactin-like proteins (PLPs), which ate distinct from the PLs, have been identified in mminants and rodents (11,23). Several cDNA transcripts coding for PLPs in catde have been identified (23). These transcripts code for proteins which possess about 40% sequence homology with bovine PRL 60% if conservative substitutions ate considered. Three glycosylated PLPs, ie, PLP-A, -B, and -C, ate produced during pregnancy in the rat (11). Two additional prolactin-related molecules have been identified in the mouse (24,25), ie, proliferin [92769-12-5] (PLF) and PLF-related protein [98724-27-7]. These ate not found in other rodents and may be unique to the mouse. The functional roles of PLPs remain to be deterrnined. 

Table 3. Sequence Homologies for Serine Proteases Involved in Coagulation and Fibrinolysis ...

SY Chung, S Subbiah. A structural explanation for the twilight zone of protein sequence homology. Structure 4 1123-1127, 1996. 

K Sjdlander, K Karplus, M Brown, R Hughey, A Krogh, IS Mian, D Haussler. Dirichlet mixtures A method for improved detection of weak but significant protein sequence homology. Comput Appl Biosci 12 327-345, 1996. 

Several motifs usually combine to form compact globular structures, which are called domains. In this book we will use the term tertiary structure as a common term both for the way motifs are arranged into domain structures and for the way a single polypeptide chain folds into one or several domains. In all cases examined so far it has been found that if there is significant amino acid sequence homology in two domains in different proteins, these domains have similar tertiary structures. 

One might expect these positions to exhibit a higher degree of amino acid conservation and hence sequence homology than the rest of the molecule. This is not, however, the case for distantly related molecules that have low sequence homology and derive from distantly related species. The sequence identity of these residues is no greater than in the rest of the... 

In Bacillus snbtilis these two reactions are catalyzed by two separate enzymes that have amino acid sequences homologous to the corresponding regions of the bifunctional enzyme from E. coli, and thus each forms a barrel... 

There is a second family of small lipid-binding proteins, the P2 family, which include among others cellular retinol- and fatty acid-binding proteins as well as a protein, P2, from myelin in the peripheral nervous system. However, members of this second family have ten antiparallel p strands in their barrels compared with the eight strands found in the barrels of the RBP superfamily. Members of the P2 family show no amino acid sequence homology to members of the RBP superfamily. Nevertheless, their three-dimensional structures have similar architecture and topology, being up-and-down P barrels. 

This structural similarity is also reflected in the amino acid sequences of the domains, which show 40% identity. They are thus clearly homologous to each other. The motif structures within the domains superpose equally well but their sequence homology is less, being around 30% between motifs 1 and 2 and 20 Xi between 3 and 4. This study, however, clearly shows that the topological description in terms of four Greek key motifs is also valid at the structural and amino acid sequence levels. 

The C-terminal domain of phosducin is a five-stranded mixed p sheet with a helices on both sides, similar to the thioredoxin fold of disulfide iso-merase DsbA described in Chapter 6. Despite significant sequence homology to thioredoxin, the phosducin domain, unlike other members of this family. 

FIGURE 10.13 Some of the sequence homologies in the nucleotide binding and phosphorylation domains of Na, K -ATPase, Ca -ATPase, and gastric H, K -ATPase. (Adapted from j0rgensm, P. L., and Andersen, J. R, 1988. Structnral basis for Ei - E2 confoyinational transitions in Na, K -pnmp and Cc -pnmp proteins. Journal of Membrane Biology 103 95-120)... 

Cholinesterases (ChEs), polymorphic carboxyles-terases of broad substrate specificity, terminate neurotransmission at cholinergic synapses and neuromuscular junctions (NMJs). Being sensitive to inhibition by organophosphate (OP) poisons, ChEs belong to the serine hydrolases (B type). ChEs share 65% amino acid sequence homology and have similar molecular forms and active centre structures [1]. Substrate and inhibitor specificities classify ChEs into two subtypes ... 

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