Motifs sequence homology

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. 

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. 

Most of the known antiparallel p structures, including the immunoglobulins and a number of different enzymes, have barrels that comprise at least one Greek key motif. An example is 7 crystallin, which has two consecutive Greek key motifs in each of two barrel domains. These four motifs are homologous in terms of both their three-dimensional structure and amino acid sequence and are thus evolutionarily related. 

In the aligned primary structures of class I decarboxylases, the conserved amino acid residues are scattered over their primary structures. There have been few reports to identify the amino acid residues essential for catalytic activity or substrate binding. Huang et al. reported the E-X-P motif in the alignment analysis for 4-hydroxybenzoate decarboxylase of C. hydroxybenzoicum and its homologous unidentified proteins. The E-X-P motif is also conserved in pyrrole-2-carboxylate decarboxylase and indole-3-carboxylate decarboxylase (unpublished data). However, the corresponding motif sequence is not observed in the primary structures of 3,4-dihydroxybenzoate decarboxylase of E. cloacae P241. ... 

The gene encoding PBAN was first characterized from H. zea and B. mori [134,137,138,195]. The cDNA was found to encode the 33 amino acid PBAN plus four additional peptides with a common C-terminal FXPRL sequence motif, including that of the diapause hormone of B. mori (Fig. 6). Three additional peptides with the common C-termini and sequence homology to those of H. zea and B. mori have been deduced from cDNA isolated from pheromone glands of several other moths [194,196-200]. Studies conducted to find the post-translational processed peptides indicated that PBAN was found to a greater extent in the mandibular and maxillary clusters than in the labial cluster of neurons... 

A third member of this family, an extracellular oxidase, has also been identified by sequence homology (118). This homology may indicate that the (tyrosyl)Cu(II) motif is not unique for one enzyme but may represent a common structural motif for a class of enzymes. 

Other adhesion receptors that are structurally and functionally related include the receptors for fibronectin, vitronectin, platelet glycoproteins 13b and Ilia and the VLA (very-late antigen) series. All molecules involved in adhesion recognise the RGD motif and require the divalent cations Ca2+ and Mg2+ for binding. All are dimers of glycosylated proteins with relative molecular masses 95-190 kDa. There is also some sequence homology between the /J-chain (CD18) and one chain of the fibronectin receptor. 

In the area of mononuclear nonheme iron enzymes, x-ray crystal structures are now also available for the catalytic domain of human phenylalanine hydroxylase [18] and naphthalene 1,2-dioxygenase [19]. The mononuclear iron site of phenylalanine hydroxylase resembles the 2-His-l-Asp site of tyrosine hydroxylase, a result anticipated by sequence homology. More interestingly, naphthalene 1,2-dioxygenase, which catalyzes the c/ s-dihydroxylation of arene double bonds in the biodegradation of aromatics, also has a Fe(His)2(Asp) iron site. These two enzymes augment the increasing number of mononuclear nonheme iron enzymes with a common Fe(His)2(carboxylate) facial triad motif [20],... 

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