SCOP superfamilies

SUPERFAMILY [19] is a collection of profile HMMs aiming to represent all proteins of known structure. Each model corresponds to a domain described in the SCOP structural classification database and aims to describe the entire SCOP superfamily associated with the domain. 

SCOP superfamilies identify probable common evolutionary origin. Proteins whose sequences have low similarities, but that share the same fold and have similar functions, suggest that a common evolutionary origin is probable. 

The SCOP database is curated manually, with the objective of placing proteins in the correct evolutionary framework based on conserved structural features. Two similar enterprises, the CATH (class, architecture, topology, and homologous superfamily) and FSSP (/old classification based on structure-structure alignment of proteins) databases, make use of more automated methods and can provide additional information. 

For those interested in statistics, in September 1998, there were 7657 structures deposited in the Brookhaven Protein Database (http //www.pdb.bnl.gov). These are analyzed on the scop database (http //scop.mrc-lmb.cam.ac.uk) into 435 folds, 640 superfamilies, 948 families, and 14 903 domains. There are probably about 1000 different superfamilies.35... 

Brazzein, the smallest of sweet proteins, was discovered only in 1994 (Ming and Hellekant, 1994) in Pentadiplandra brazzeana B. This protein, whose sequence contains 54-amino acid residues, is 2000 times sweeter than sucrose when compared to a 2% sucrose aqueous solution. Its taste was described as more similar to sucrose than that of thaumatin (Ming and Hellekant, 1994). As can be seen in Figure 5C, the 3D structure of brazzein, determined by NMR spectroscopy in solution at pH 5.2 (Caldwell et al., 1998), is very simple. It contains one a-helix and three strands of antiparallel )3-sheet. The structure is stabilized by four disulfide bonds, three connecting the helix to the jS-sheet. It does not resemble either that of monellin or that of thaumatin instead, it resembles those of plant y-thionins and defensins and arthropod toxins. According to the SCOP classification (Murzin et al., 1995), brazzein belongs to the Scorpion toxin-like superfamily. 

Templates can be selected using the target sequence as a query for searching protein structure databases [e.g. Brookhaven Protein Data Bank (PDB) http / /www.rcsb.org/pdb/index.html Structural Classification of Proteins (SCOP) scop.mrc-lmb.cam.ac.uk/scop/ DALI www2.ebi.ac.uk/dali/ Class, Architecture, Topology and Homologous superfamily classification at CATH www.biochem.ucl.a-c.uk/bsm/cath/). 

NAD -dependent alcohol dehydrogenases (EC 1.1.1.1) are encoded in the C. elegans genome (Fig. 15.1). The list of standard PEDANT queries includes EC numbers, PROSITE patterns, Pfam domains, BLOCKS, and SCOP domains, as well as PIR keywords and PIR superfamilies. Although PEDANT does not allow the users to enter their own queries, the variety of data available at this Web site makes it a convenient entry point into the held of comparahve genome analysis. 

SCOP is a hierarchic classification with four major levels classes, folds, superfamilies, and families. As recognized by the authors of SCOP, the exact... 

Figure 11 Statistics of the SCOP classification of proteins. The numbers of folds, superfamilies, and families in SCOP are plotted against time , where time is the timestamp of the PDB used to generate the update of SCOP.

The Homologous Superfamily level, or H level, groups together protein domains thought to share a common ancestor. This level is equivalent to the superfamily level defined in SCOP. CATH also includes a Sequence Families level (S-level) that is equivalent to the family level of SCOP. 

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