Fold domain

Structure of folded domains Globular a-helix rich Not determined Not determined Not determined 1 Globular a-helix rich... 

As for HET-s, the structure of its N-terminal domain has yet to be determined however, NMR data suggest that residues 1-227 form a well-folded domain (Balguerie et al, 2003). HET-s is a special case because the prion form is the active form, so that the prion domain (residues 218-289) is needed for function. Although the prion domain alone is sufficient for prion maintenance, it is not competent in heterokaryon incompatibility. For this activity, at least HET-s157-289 must be expressed (Balguerie et al., 2004). 

Horiuchi, M., Baron, G. S., Xiong, L. W., and Caughey, B. (2001). Inhibition of interactions and interconversions of prion protein isoforms by peptide fragments from the C-terminal folded domain./. Biol. Chem. 276, 15489-15497. 

The association of secondary structures to give super-secondary structures, which frequently constitute compactly folded domains in globular proteins, is completed by the a-a motifs in which two a-helices are packed in an anti-parallel fashion, with a short connecting loop (Figure 4.8c). Examples of these three structural domains, often referred to as folds, are illustrated in Figures 4.9—4.11. The schematic representation of the main chains of proteins, introduced by Jane Richardson, is used with the polypeptide backbone... 

This section describes an example of the application of PSSMs to structure prediction that involves two previously undetected families of OB (oligomer-binding) fold domains. The OB folds were first identified... 

Transitive, iterative searches initiated with the sequences of the anticodon-binding domains of lysyl- and aspartyl-tRNA synthetases provided leads for the identification of biologically interesting, previously unknown OB-fold domains at a statistically significant level (random expectation values <0.01). In particular, OB folds were detected in the eukaryotic replication factor RFA with statistically significant scores this... 

Fig. 1. Structure of the OB-fold domain. The anticodon-binding domain of the E. coli lysyl-tRNA synthetase (pdb code lkrs) is shown as a prototype of single-stranded nucleic acid-binding OB-folds. The model was drawn using the Molscript v2.1 program...

The alignment of these predicted OB-fold domains is consistent with a conserved arrangement of the secondary structure elements that are seen in the ModE structure and suggests that all members of this family form an interlocked structure (Fig. 2B,C). Furthermore, secondary structure... 

In each of the three divisions of life, the most common fold is the P-loop NTPase. Four common folds, namely P-loop NTPases, Triose Phosphate Isomerase (TIM) barrels, ferredoxin-like domains, and Rossmann-fold domains, are see in the top-10 lists for all three divisions (Table IV). 

A more detailed breakdown of the fold abundance by individual genomes shows the same trends, as well as a number of unique features (Fig. 6, see color insert). The latter include, for example, the marked overrepresentation of Rossmann-fold domains in Mycobacterium, flavo-doxins in Synechocystis and methyltransferases in Helicobacter. Furthermore, the differences in fold distribution between the multicellular eukaryote Caenorhabditis elegans and the unicellular yeast become readily apparent. In the nematode, the protein kinases are the most common fold, with the P-loops relegated to the second position in contrast, the yeast distribution is more similar to that seen in prokaryotes (Fig. 6). 

Figure 1. Variants of the histones H3 from yeast Saccharomyces cerevisiae S.c.), fruit fly Drosophila melanogaster D.m), and human Homo sapiens H.s.). H3.1 is identical to H3.2 with the exception of a serine to cysteine exchange (top). H3.3 differs from H3.1/H3.2 only in four amino acid positions. Centromer-specific histones (CenH3 s) have an amino terminus of variable length (between 20 and 200 residues). They also possess an extended loop 1 region in the histone fold domain...

Although the histone fold was first described from the structure of the histone octamer core of the nucleosome [17], the high a-helical content was predicted much earlier [43]. The core histones possess three functional domains (1) the histone fold domain, (2) an N-terminal tail domain, and (3) various accessory helices and less structured regions. The N-terminal tail domains of the core histones are currently the focus of intense research. Covalent modifications of residues in these unstructured domains appear to modify local chromatin structure, either directly or... 

Despite many biochemical similarities between linker and core histones the proteins of these two groups differ in architecture, evolutionary origin, and function. Each of the four core histones has a characteristic histone fold domain. The latter is an old and ubiquitous structural motif used in DNA compaction and protein dimerization [3]. Linker histones do not have a histone fold. The canonical... 

Sullivan, K.F., Hechenberger, M., and Masri, K. (1994) Human CENP-A contains a histone H3 related histone fold domain that is required for targeting to the centromere. J. Cell Biol. 127, 581-592. Choo, K.H. (2000) Centromerization. Trends Cell Biol. 10, 182-188. 

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