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Clade A group of organisms or molecules, whose members share homologous features derived from a common ancestor. Cluster analysis A data analysis tool for solving classification problems. Organisms or molecules are sorted into clusters, so that the degree of association is strong between members of the same and weak between members AAA Proteins Complex cellular events commonly depend on the activity of molecular machines that efficiently couple enzymatic and regulatory functions within a multiprotein assembly.

Nucleotide and coordination of a Mg2þ-ion, which is important for subsequent hydrolysis of ATP. It is a RecA-like, threelayered aba structure with a central five-stranded, parallel b sheet. The property that separates this fold from that of all other P-loop NTPases is the insertion of a b strand which results in the addition of a conserved polar residue to the active site. The residue has been named sensor-1 for the fact that it contacts the g-phosphate of the bound nucleotide and is thought to discriminate between ATP and ADP.

The carboxy-terminal subdomain is largely helical and shows substantially greater structural variation, although it invariably occupies a similar position, diagonally above the base of the bound nucleotide. A recurring feature of this subdomain is a residue (typically arginine), called sensor-2 for its ability to interact with the nucleotide. Depending on the subtype of AAA proteins, either one or two AAA domains (D1 and D2) are present. In some proteins with two domains, both are evolutionarily well conserved (like in Cdc48p/p97); in others, either the D2 domain (like in Pex1p and Pex6p) or the D1 domain (in Sec18p/NSF) is better conserved.