P Thymidylate synthase/dCMP hydroxymethylase Thymidylate synthase/dCMP hydroxymethylase Thymidylate synthase/dCMP hydroxymethylase Thymidylate synthase

Escherichia coli

1EMA GFP-like GFP-like

Fluorescent proteins

Green fluorescent protein, GFP

Jellyfish (Aequorea victoria)

PDB identifier Fold

Superfamily Family Protein Species

FIGURE 4-22 Organization of proteins based on motifs. Shown here are just a small number of the hundreds of known stable motifs. They are divided into four classes: all a, all p, a/p, and a + p. Structural classification data from the SCOP (Structural Classification of Proteins) database (http://scop.mrc-lmb.cam.ac.uk/scop) are also provided. The PDB identifier is the unique number given to each structure archived in the Protein Data Bank (www.rcsb.org/pdb). The a/p barrel, shown in Figure 4-21, is another particularly common a/p motif.

motif and have functional similarities; these families are grouped as superfamilies. An evolutionary relationship between the families in a superfamily is considered probable, even though time and functional distinctions—hence different adaptive pressures—may have erased many of the telltale sequence relationships. A protein family may be widespread in all three domains of cellular life, the Bacteria, Archaea, and Eukarya, suggesting a very ancient origin. Other families may be present in only a small group of organisms, indicating that the structure arose more recently. Tracing the natural history of structural motifs, using structural classifications in databases such as SCOP, provides a powerful complement to sequence analyses in tracing many evolutionary relationships.

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.

Structural motifs become especially important in defining protein families and superfamilies. Improved classification and comparison systems for proteins lead inevitably to the elucidation of new functional relationships. Given the central role of proteins in living systems, these structural comparisons can help illuminate every aspect of biochemistry, from the evolution of individual proteins to the evolutionary history of complete metabolic pathways.

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