Domain arrangement

Figure 10.23 Domain arrangement along the polypeptide chains of three families of transcription factors b/z, b/HLH and b/HLH/z. All three have a basic region (blue) that binds DNA. Dimerization is achieved by the zipper region (purple) in the b/z family, by the Hl-loop-H2 region (red-yellow-green) in the b/HLH family and by a combination of both the zipper and the HLH regions in the b/HLH/z family.

Total Number of Domains Arrange- ment Bonding Domains Lone Pair Domains Geometry Examples ... 

Binda, C., Bossi, R. T., Wakatsuki, S., Arzt, S., Coda, A., Curti, B., Vanoni, M. A., and Mattevi, A. (2000). Cross-talk and ammonia channeling between active centers in the unexpected domain arrangement of glutamate synthase. Structure 8, 1299-1308. 

An in-depth study of DNA repair systems (Aravind et al., 1999a) has concluded that few, if any, repair proteins occur with identical collinear domain arrangements in all three kingdoms of life. Approximately 10 enzyme families of adenosine triphosphatases (ATPases), photolyases, helicases, and nucleases were identified that are all likely to have been present in the cenancestor. These enzymatic domains are accompanied in DNA repair proteins by numerous regulatory domains. This indicates that the domain architectures of these proteins are labile, with incremental addition and/or subtraction of domains to conserved cores to be a common phenomenon except in the most closely related species. 

Shot Ribbon and lenticular anisotropic domains arranged in concentric patterns to form shotlike coke... 

SAXS measurements with CBH II indicated a very similar tertiary structure for both CBH I and CBH II, in spite of a different domain arrangement (to be published). Discrete differences in the tail parts could, however, be noticed. The maximum diameter of CBH II (21.5 nm) was higher than in CBH I this might be due to duplication of the glycosylated part in the former case. Thus, the functional differentiation of these cellulases can be reflected by structural differences. 

Our chromophoric substrates proved to be valuable in the study of several aspects of the enzymology of these cellulases. A rapid and specific method for purification (affinity chromatography) has been developed. Following our collaboration with several groups, new insights into the domain arrangement and tertiary structures of two cellulases were obtained. Contributions to the elucidation of the synergistic action (adsorption-hydrolysis) of these enzymes were achieved. 

Fig. 17. (a) Schematic of the trimeric arrangement of NIR. (b) Hypothetical domain arrangement in ceruloplasmin. L, Lysine. 

MA Tavanlar. Molecular characterisation of the 8-(L-a-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS) from filamentous fungi determination of the domain arrangement, cloning and expression of the third domain. Ph.D. thesis, University of Los Banos/Technical University of Berlin, 1996. 

Two crystalline forms of ascorbate oxidase from zucchini (Messerschmidt et al., 1989) have been analysed at 2.5 A resolution and a model of the polypeptide chain and the copper ions and their ligands has been prepared. The crystal forms M2 and Ml contain a dimer of 140000 Mr and a tetramer of 280000 Mr in the asymmetric unit. Each subunit of about 550 amino acid residues has a globular shape with dimensions of 49 A x 53 A x 65 A. The subunit has three domains arranged sequentially... 

The third ABC protein believed to play a role in clinical MDR, ABCG2 (MXR/BCRP) is a half transporter [15,34], with a unique domain arrangement, where the ABC is located at the N-lerminus (Fig. 2). This protein performs an active extrusion of hydrophobic, positively charged molecules... 

Calcium channels are present in nerve terminals and muscles. They consist of four homologous domains arranged symmetrically around a central ion pore (Figure 7.11 and 712). Therefore, calcium and sodium channels share the basic structure of these repeat domains (I—IV). Under normal conditions, muscle contraction is mediated by calcium channels, as shown in the following text. Depolarization caused by an action potential in the motor nerve terminal activates calcium channels and triggers an influx of Ca2+ ions. These ions... 

Bomberg-Bauer, E., Beaussart, F., Kummerfeld, S.K., Teichmann, S.A. and Weiner, J. 3rd (2005) The evolution of domain arrangements in proteins and interaction networks. Cell Mol. Life Sci. 62, 435 45. 

Comoviridae—Coat protein(s) form a 320-A-diameter T=1 capsid. Protein(s) contains three homologous domains, arranged with... 

The subunits are arranged in the crystals as homotetramers with D2 symmetry. The structure of a subunit is shown schematically in Fig. 1 (87). Each subunit of 552 amino acid residues has a globular shape with dimensions of 49 x 53 x 65 A and is built up of three domains arranged sequentially on the polypeptide chain, tightly associated in space. The folding of all three domains is of a similar jS-barrel type. It is distantly related to the small blue copper proteins, for example, plastocyanin or azurin. Domain 1 is made up of two four-stranded jS-sheets (Fig. lb), which form a jS-sandwich structure. Domain 2 consists of a six-stranded and a five-stranded jS-sheet. Finally, domain 3 is built up of two five-stranded jS-sheets that form the jS-barrel structure and a four-stranded j8-sheet that is an extension at the N-terminal part of this domain. A topology diagram of ascorbate oxidase for all three domains and of the related structures of plastocyanin and azurin is shown in Fig. 2. Ascorbate oxidase contains seven helices. Domain 2 has a short a-helix (aj) between strands A2 and B2. Domain 3 exhibits five short a-helices that are located between strands D3 and E3 (a ), 13 and J3 (a ), and M3 and N3 (a ) as well as at the C terminus (ag and a ). Helix 2 connects domain 2 and domain 3. 

In most specimens, albite twinning predominates over pericline twinning. Generally, the albite twinning is on a very fine scale and occurs in domains separated by untwinned domains, arranged to form several types of overall microstructure (McLaren 1984). 

Figure 24 NRPS module skipping mechanism revealed by myxochromides A and S biosynthesis, (a) Myxochromides A and S structures and module and domain arrangement in their biosynthetic machineries, (b) Proposed NRPS-module skipping mechanism by loss-of-function mutation in T domain of the skipped module.

Ly, Y.P., and Cheng, Y.-L. 1997. Diffusion in heterogeneous media containing impermeable domains arranged in parallel arrays of variable orientation. Journal of Membrane Science 133, 207-215. 

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