Head domains

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).

B. Adenovirus, Reovirus, and Phage PRD1 Fiber Head Domains. 99... 

Fig. 1. Schematic drawings of the viruses discussed in this chapter. (A) An icosahe-dral virus with fiber proteins inserted in its pentameric vertices. The gray box denotes domains with known structures for adenovirus, reovirus, and bacteriophage PRD1, in each case containing the head domain and proximal part of the triple /8-spiral shaft domain. (B) Contractile-tailed bacteriophage T4. T4 contains three different fibrous proteins, fibritin connected to the neck, the long (bent) fibers connected to the base plate, and the short fibers also connected to the base plate. Only two of each of the trimeric fibrous proteins are shown for clarity. The gray box denotes domains with known structure for the T4 short fiber.

Fig. 2. Adenovirus fiber head domain. (A) Adenovirus type 12 fiber head seen from the side (PDB-code 1NOB Bewley et al., 1999). The three monomers are colored differendy. (B) Adenovirus type 12 fiber head domain bound to CAR D1 seen from the top (PDB-code 1KAC Bewley et al., 1999). Here, the adenovirus type 12 trimer is shown in yellow and the CAR D1 domain in purple. Figures 2-5 were produced using PyMOL (DeLano, 2002).

More recently, triple /1-spiral repeats have been identified in mammalian reovirus type 3 fiber (Chappell et al., 2002 Fig. 4A), avian reovirus fiber (Guardado Calvo et al., 2005 Fig. 4B), and bacteriophage PRD1 P5 protein (Merckel et al., 2005 Fig. 4C). In the latter two cases, it appears that only two repeats are present, just N-terminal to the head domain. Mammalian reovirus fiber contains eight putative triple /1-spiral repeats, of which three were resolved in the crystal structure (Chappell et al., 2002). 

The T4 short tail fiber triple /l-helix is connected to a more globular head domain via residues 333-341, which form a very short a-helical triple coiled-coil. Residues 342-396, together with the C-terminal /1-strand composed of amino acids 518-527 (the collar ), are the only part of the structure in which the monomer has a recognizable fold. It may therefore be the first part of the protein to fold, followed by a zipping-up of the N-terminal domain and the top domain. The small, globular, domain contains six /1-strands and one a-helix and has some structural homology to gpl 1, also of bacteriophage T4. Three of the /1-strands and the a-helix formed by residues... 

The condensin complex has been identified in the same scaffold fraction (Maeshima and Laemmli, 2003) and shown to be essential for the mitotic chromosome condensation (Hirano et al, 1997). The frog condensin complex exhibits ATP-dependent DNA-supercoiling activity (Kimura and Hirano, 1997). It consists of a heterodimer of SMC and a trimer of non-SMC proteins (Hirano et al, 1997). The SMC complex has a globular head domain and a coiled-coil tail region (Anderson et al., 2002 Melby et al, 1998 Yoshimura et al., 2002). In vertebrates, two types of condensin complex, condensin I and condensin II, exist they are composed of the same SMC subunits but with different non-SMC subunits (Ono et al, 2003). 

CBH I 497 core-BA aa sequence in part from protein and in full from gene (cbhl), number and location of SS bridges, region of O-glycosylation, types of carbohydrate, papain cleavage site, hydrophobic cluster analysis, computer model of active site, 2D-NMR on a synthetic tail fragment, SAXS on whole CBH I, head domain and xylan/CBH I complex... 

It can be assumed that the amino acids following this hinge region (Val 93 to Leu 447) are part of the head domain. The point of papain cleavage is at amino acid 82 27. TTie core part of the polypeptide chain is mainly folded in )3-sheets (34 %) and to a lesser extent (15 %) arranged in alpha-helical structures 7. In contrast with CBH I the core of CBH II possesses only 2 disulfide bridges (176-235 368-415) and four free sulfhydryl groups. Similarly to CBH I carboxyl functions are involved in the active center (Asp 175 and Glu 184) 28. 

The head domain in trichocyte (or hair) keratins has been characterized by Parry and North (1998) and Parry et al. (2002) and shown to consist of two domains—a basic one (NB) at the N-terminal end of the head domain (27 and 70 residues long, respectively, for Type I and Type II chains) and an acidic one (NA) lying between the rod and NB. The latter is 29 and 34 residues long for Type I and Type II chains, respectively. Importantly, however, NA is homologous to HI in the respective chain types of epidermal keratins. There can therefore be little, if any, doubt that the role of these regions in trichocyte and epidermal keratins is... 

In the Type II head domains, the sequences display little homology over the first 12 residues but there is considerable consensus over the next 24 (residues 13-36). This sequence is R-A-F-S-C-V-S-A-C-G—P-R-P—... 

In many respects, the linker LI can be likened to a flexible hinge, a role consistent with a swinging head model proposed for IFs. In this model, segment 1A can (under appropriate conditions) split into two separate Q-helical strands, thereby maximizing the range of movement of the head domains and hence increasing their capacity to interact with various other cellular entities (Parry et al, 2002). 

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