Structure domain organization

In this chapter we describe some examples of structures of membrane-bound proteins known to high resolution, and outline how the elucidation of these structures has contributed to understanding the specific function of these proteins, as well as some general principles for the construction of membrane-bound proteins. In Chapter 13 we describe some examples of the domain organization of receptor families and their associated proteins involved in signal transduction through the membrane. 

C. Description of the Molecular Structure of the Fepr Protein 1. The Domain Organization of the Fepr Molecule... 

The equivalent of the tryptic fragment of human transferrin receptor has been expressed in Chinese hamster ovary cells and its structure determined at a resolution of 0.32 nm (Lawrence et ah, 1999). The asymmetric unit of the crystals contains four transferrin receptor dimers. Interpretable electron density is found for the entire tryptic fragment except for Arg-121 at the amino terminus, and density is also seen for the first N-acetylglucosamine residue at each of the N-glycosylation sites. The transferrin receptor monomer is made up of three distinct domains, organized such that the dimer is butterfly shaped (Figure 5.10, Plate 7). The likely orientation of the dimer with respect to the plasma membrane has been assigned on the basis of the... 

Figure 1. (a) A schematic representation of the overall organization of the molecule of human ceruloplasmin. Domains 2,4, and 6 contain mononuclear copper centers, while the trinuclear copper cluster is located at the interface of domains 1 and 6. (b) An a-carbon ribbon diagram of the human ceruloplasmin molecule viewed along the pseudo threefold axis highlighting the triplication of the structure. Domains 1, 3, and 5 are depicted by striped motifs, whereas domains 2, 4, and 6 are dark shaded. The copper... 

Balguerie, A., Dos Reis, S., Ritter, C., Chaignepain, S., Coulary-Salin, B., Forge, V., Bathany, K., Lascu, I., Schmitter, J. M., Riek, R., and Saupe, S. J. (2003). Domain organization and structure-function relationship of the HET-s prion protein of Podospora anserina. EMBO J. 22, 2071-2081. 

It can be difficult if not impossible to find the domain structure of a protein of interest from the primary literature. The sequence may contain many common domains, but these are usually not apparent from searches of literature. Articles defining new domains may include the protein, but only in an alignment figure, which are not searchable. Perhaps, with the advent of online access to articles, the full text including figures may become searchable. Fortunately there have been several attempts to make this hidden information available in away that can be easily searched. These resources, called domain family databases, are exemplified by Prosite, Pfam, Prints, and SMART. These databases gather information from the literature about common domains and make it searchable in a variety of ways. They usually allow a researcher to look at the domain organization of proteins in the sequence database that have been precalculated and also provide a way to search new sequences... 

The largest grouping of structures contains domains organized around a parallel or mixed j8 sheet, the connections for which form structure (usually helical) protecting both sides of the sheet, with the... 

The structurally related myxochromides Aj.j are cyclic hexapeptides produced by several Myxococcus species. These examples contain a proline residue, which is not present in myxochromides Si 3, as the fourth amino acid in their peptide core. The NRPSs responsible for myxochromides A and S biosynthesis have exacdy the same module and domain organization thus, the fourth module of the myxochromide S synthetase must be skipped to account for the natural product. Biochemical experiments revealed that the A domain of this module activates L-proline, but the adjacent PCP domain cannot be phosphopantetheinylated by a PPTase. These results suggest that the C domain of module 5 reacts directly with the tripeptide intermediate bound to the PCP domain of module 3 in myxochromide S biosynthesis. A similar example of domain skipping has been noted in the biosynthesis of the mannopeptimycins. ... 

The hammerhead motif has a conserved secondary structure consisting of a three-way helical junction. The helical elements may vary in base sequence among species but thirteen bases at the three-way helical junction are conserved and essential for ribozyme activity. X-ray structures to be discussed below define a domain organization based on the tertiary folding observed in... 

Detailed pictures of the iron-binding sites in transferrins have been provided by the crystal structures of lactoferrin (Anderson et ai, 1987, 1989 Baker etai, 1987) and serum transferrin (Bailey etal., 1988). Each structure is organized into two lobes of similar structure (the amino- and carboxy-terminal lobes) that exhibit internal sequence homology. Each lobe, in turn, is organized into two domains separated by a cleft (Fig. 3 and 10). The domains have similar folding patterns of the a//3 type. One iron site is present in each lobe, which occupies equivalent positions in the interdomain cleft. The same sets of residues serve as iron ligands to the two sites two tyrosines, one histidine, and one aspartate. Additional extra density completes the octahedral coordination of the iron and presumably corresponds to an anion and/or bound water. The iron sites are buried about 10 A below the protein surface and are inaccessible to solvent. 

Figure 4-4. The domain organization of an integral, transmembrane protein as well as the mechanisms for interaction of proteins with membranes. The numbers illustrate the various ways by which proteins can associate with membranes I, multiple transmembrane domains formed of a-helices 2, a pore-forming structure composed of multiple transmembrane domains 3, a transmembrane protein with a single a-helical membrane-spanning domain 4, a protein bound to the membrane by insertion into the bilayer of a covalently attached fatty acid (from the inside) or 5, a glycosyl phosphatidylinositol anchor (from the outside) 6, a protein composed only of an extracellular domain and a membrane-embedded nonpolar tail 7, a peripheral membrane protein noncova-lently bound to an integral membrane protein.

Fig. 8.12B. Structure of c-Src kinase phosphorylated at Tyrosine 527. Ribbon diagram showing the structure and organization of the closed conformation" of c-Src kinase. Two aspects of the structure are important for the regulation of c-Src kinase i) The phosphorylated Tyr 527 of the C-terminal tail is engaged in an intramolecular interaction with the SH2 domain, ii) The SH3 domain binds to the linker between the SH2 domain and the kinase domain. Both interactions are assumed to fix an inactive state of the kinase.

The enzyme is organized into two structural domains,201 one of which binds FAD and the other NADP+. Similar single-electron transfers through flavoproteins also occur in many other enzymes. Chorismate mutase, an important enzyme in biosynthesis of aromatic rings (Chapter 25), contains bound FMN. Its function is unclear but involves formation of a neutral flavin radical.276 277... 

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