Sequence comparison domains

When the crystal structure of EF-G GDP was solved, it revealed a surprising and elegant structural feature. Elongation factor G consists of five structural domains, and from sequence comparisons Domains 1 and 2 were expected to be similar in conformation to EF-Tu Domains 1 and 2. This conformational mimic does indeed occur. Domains 3 and 5 of EF-G contain protein folds similar to some ribosomal proteins whose structures are known, while Domain 4 adopts an unusual fold. This domain is elongated and points away from the rest of the protein. 

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).

In sequence comparison, common protein domains such as the tyrosine kinase domain can mask other interesting matches (Sonnhammer and Durbin, 1994). Other weak but interesting matches may be lost in a large list of matches to the common domain. Thus domain databases are a useful way to identify these common domains so that they can be removed or masked in the sequence to allow the detection of weaker or less common domain similarities. 

The salient features of A. faecalis pseudoazurin are that (1) it has a Cu-Met bond length shorter than that of either plastocyanin or azurin (see Table III) (2) it has only one NH - S bond, as does plastocyanin and (3) its overall architecture resembles plastocyanin (see Fig. 4), with an extended carboxy terminus folded into two a helices [a preliminary sequence comparison suggested that the folding would resemble plastocyanin (Adman, 1985)]. It retains the exposed hydrophobic face found in azurin and plastocyanin. Just how it interacts with nitrite reductase is still a subject of investigation. It is intriguing that the carboxy-terminal portion folds up onto the face of the molecule where the unique portions of other blue proteins are the flap in azurin, and, as we see below in the multi-copper oxidase, entire domains. 

Extensive deletion and mutation studies, as well as sequence comparisons, have shown that the nuclear receptors are constructed modularly. At the level of the primary structure the steroid hormone receptors can be divided into five different domains (fig. 4.5), each with specific functions. 

The structure of the mSos protein (m=mammalian) is shown in Fig. 9.8. Sequence comparison with known Ras-specific GEFs has identified a common domain of ca.200 amino acids, to which nucleotide exchange activity has been assigned. Within this domain, three highly conserved sequence elements can be differentiated, separated by more variable sections. Other structural elements include a PH domain and a Pro-rich binding domain. The Pro-rich sequence fimctions as an attachment site for the SH3 group of Grb2 protein. 

Protein design by site-directed mutagenesis on pyruvate decarboxylase became possible after the 3D-structure of the enzyme from Saccharomyces uvarum had become available [35], Based on sequence comparison and secondary structure prediction, the 3D-structure of the yeast enzyme served as a model for PDCZ.m. [163], The point mutations which have been introduced into the two enzymes (Tables 4 and 5) concern catalytically important residues as well as significant side-chain interactions at the domain interface of the dimer. Besides, site-directed mutagenesis offered a powerful tool to improve the car-boligase reaction of PDCZ.m. with respect to the synthesis of (P)-PAC [163,164,170]. 

The LBD has been defined as residues 114-427 at the C-terminal end of VDR [241]. Residues 403-427 are apparently important for maximal ligand affinity, whereas the other 200-300 bases are involved in ligand recognition [241]. Forman and Samuels [242] performed a sequence comparison of the extreme most portion of the C-terminal domain for several steroid receptors and found that this sequence is unique to each receptor, which is indicative... 

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