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. 

Figure 14.5 The domain organization of intermediate filament protein monomers. Most intermediate filament proteins share a similar rod domain that is usually about 310 amino acids long and forms an extended a helix. The amino-terminal and carboxy-terminal domains are non-a-helical and vary greatly in size and sequence in different intermediate filaments.

Matrix Metalloproteinases. Figure 1 Domain organization of different mammalian MMPs. 

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

FIGURE 8.3 Domain organization of proteins that associate with phosphorylated tyrosine kinase (PTK)-containing receptors. Proteins that associate with tyrosine-phosphorylated receptors contain SH2 or PTB domains, which recognize specific amino-acid stretches in the vicinity of phosphorylated tyrosine residues. Unlike the enzymes, the adaptors lack intrinsic catalytic activity but serve to link phosphorylated receptors with other effector proteins. Some of the proteins presented in this figure are discussed in this chapter. 

For the first group (i.e. intracellular soluble enzymes and proteins), which need no posttranslational modification and complex domain organization influencing protein folding, E. coli is the most preferred choice. However, for the other targets, alternative expression systems often provide a higher rate of success. The most common expression systems are presented in this chapter. 

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... 

Tsuji, Y Shimada, Y Takeshita, T et al. (2000) Cryptic dimer interface and domain organization of the extracellular region of metabotropic glutamate receptor subtype 1../. Biol. Chem. 275, 28144-28151. 

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. 

SEARCHING DATABASES TO FIND PROTEIN DOMAIN ORGANIZATION... 

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... 

Fig. 65. The dumbbell domain organization of phosphoglycerate kinase, with a relatively narrow neck between two well-separated domains.

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... 

Medved, L.V., M. Migliorini, I. Mikhailenko, L.G. Barrientos, M. Llinas, and D.K. Strickland. 1999. Domain organization of the 39-kDa receptor-associated protein. J Biol Chem 274 111-121. 

In linear NRPSs a product consisting of amino acids is biosynthesized in an N- to C-terminal manner by the multidomain assembly line with a domain organization of A-PCP-(C-A-PCP) i-TE. The initiation module of a linear NRPS lacks a C domain, while the following modules may include any required additional domains. After formation of the full-length peptide, the product is released from the assembly line by a termination domain. Thus, the number and order of amino acids in the peptide directly coincides with the number and order of synthetase modules. Many NRPs are biosynthesized in this manner, and characterized examples include the penicillin tripeptide precursor -(L-0 -aminoadipyl)-L-cysteinyl-D-valine (ACV, Figure 4 (a)), complestatin, cyclosporin, fengycin, surfactin, and tyrocidine. "... 

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 oxidation state of thiazolines and oxazolines can be adjusted by additional tailoring enzymes. For instance, oxidation domains (Ox) composed of approximately 250 amino acids utilize the cofactor FMN (flavin mononucleotide) to form aromatic oxazoles and thiazoles from oxazolines and thiazolines, respectively. Such domains are likely utilized in the biosynthesis of the disorazoles, " diazonimides, bleomycin, and epothiolone. The typical domain organization for a synthetase containing an oxidation domain is Cy-A-PCP-Ox however, in myxothiazol biosynthesis one oxidation domain is incorporated into an A domain. Alternatively, NRPSs can utilize NAD(P)H reductase domains to convert thiazolines and oxazolines into thiazolidines and oxazolidines, respectively. For instance, PchC is a reductase domain from the pyochelin biosynthetic pathway that acts in trans to reduce a thiazolyinyl-Y-PCP-bound intermediate to the corresponding thiazolidynyl-Y-PCP. ... 

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... 

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