A/p domains

On the basis of simple considerations of connected motifs, Michael Leviff and Cyrus Chothia of the MRC Laboratory of Molecular Biology derived a taxonomy of protein structures and have classified domain structures into three main groups a domains, p domains, and a/p domains. In ct structures the core is built up exclusively from a helices (see Figure 2.9) in p structures the core comprises antiparallel p sheets and are usually two P sheets packed... 

The most frequent of the domain structures are the alpha/beta (a/P) domains, which consist of a central parallel or mixed P sheet surrounded by a helices. All the glycolytic enzymes are a/p structures as are many other enzymes as well as proteins that bind and transport metabolites. In a/p domains, binding crevices are formed by loop regions. These regions do not contribute to the structural stability of the fold but participate in binding and catalytic action. 

Figure 4.13 (a) The active site in open twisted a/p domains is in a crevice outside the carboxy ends of the P strands. This crevice is formed by two adjacent loop regions that connect the two strands with a helices on opposite sides of the P sheet. This is illustrated by the curled fingers of two hands (b), where the top halves of the fingers represent loop regions and the bottom halves represent the P strands. The rod represents a bound molecule in the binding... 

Figure 4.21 The polypeptide chain of the arabinose-binding protein in E. coli contains two open twisted a/P domains of similar structure. A schematic diagram of one of these domains is shown in (a). The two domains are oriented such that the carboxy ends of the parallel P strands face each other on opposite sides of a crevice in which the sugar molecule binds, as illustrated in the topology diagram (b). [(a) Adapted from J. Richardson.)...

Figure 14.13 Stmcture of G-actin. Two a/P-domains, (red and green) bind an ATP molecuie between them. Tbis ATP is hydrolyzed when the actin monomer polymerizes to F-actin.

Fig. 93. Topology diagrams for the doubly wound and miscellaneous a/p domains illustrated in Figs. 76 through 78. Arrows represent the P strands thin connections lie behind the p sheet and fat ones above it. The darkest upper box surrounds the classic doubly wound sheets successively lighter solid boxes include domains that are progressively less like the classic topology the dotted box encloses the miscellaneous a/P structures. K = kinase P = phospho DH = dehydrogenase ATCase = aspartate transcarbamylase.

Prokaryotic initiation factors. In addition to the ribosomal proteins, the initiation factors IFl, IF2, and IF3, whose molecular masses are 9.5, 9.7, and 19.7 kDa, respectively, " are essential. They coordinate a sequence of reactions that begins with the dissociation of 70S ribosomes into their 30S and 50S subunits. Then, as is shown in Fig. 29-10, the mRNA, the initiator tRNA charged with formylmethionine, the three initiation factors, and the ribosomal subunits react to form 70S programmed ribosomes, which carry the bound mRNA and are ready to initiate protein synthesis. IF2 is a specialized G protein (Chapter 11), which binds and hydrolyzes GTP. It resembles the better known elongation factor EF-Tu (Section 2). The 172-residue IF3 consists of two compact a/p domains linked by a flexible sequence, which may exist as an a Its C-terminal domain binds to the central domain of the 16S RNA near nucleotides 819-859 (Fig. 

Once proteins are divided into domains the domains are then classified hierarchically. At the top of the classification we usually find the class of a protein domain, which is generally determined from its overall composition in secondary structure elements. Three main classes of protein domains exist mainly a domains, mainly (3 domains, and mixed a p domains (the domains in the a — p class are sometimes subdivided into domains with alternating a/p secondary structures and domains with mixed a + p secondary structures). In each class, domains are clustered into folds according to their topology. A fold is determined from the number, arrangement, and connectivity of the domain s secondary structure elements. The folds are subdivided into superfamilies. A superfamily contains protein domains with similar functions, which suggests a common ancestry, often in the absence of detectable sequence similarity. Sequence information defines families, i.e., subclasses of superfamilies that regroup domains whose sequences are similar. 

This chaperone is involved in the folding of proteins with a molecular weight of 20 to 60 KDa and contributes to forming the proper structures of about 10 % to 15 % of all proteins expressed in a cell (Ewalt et al. 1997). Polypeptides with an a/p domain structure have been shown to preferably attach to this chaperone for folding. 

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