Structures of the AAA+ modules of selected superfamilymembers (see Table 1). The core αβα nucleotide-binding domains are shown in green (α-helices and random coil) and blue (β-strands). The small, α-helical domain of each AAA+ module is shown in purple. The canonical AAA+ module structure is exemplified by that of RFC1, which is shown in the center. (a) Representative members of the extended AAA group . The FtsH AAA+ module from Thermus thermophilus (left, PDB 2DHR) contains an additional small helix (pink) downstream of the second β-strand, which is characteristic of the classical AAA clade [1,15]. The function of FtsH is discussed in the text. The Rvb AAA+ module, represented by human Rvb1 (center, PDB 2C90), contains a β-sheet-rich insert (pink) upstream of the Walker B motif and an additional small helix (yellow) downstream of the second β-strand of the core domain . The β-sheet-rich insert is proposed to play a role in sequence-independent DNA and RNA binding . The amino-terminal (D1) AAA+ modules of ClpB-type proteins are represented by a structure from T. thermophilus (right, PDB 1QVR). These proteins contain a long, leucine-rich coiled-coil propeller domain (pink) inserted into the small α-helical domain . This propeller domain is proposed to play a role in interdomain communication and protein disaggregation, possibly acting as a molecular crowbar . (b) Representative members of the HEC group . The RFC1 AAA+ module from S. cerevisiae (center, PDB 1SXJ) represents a 'classical' AAA+ module containing no structural modifications and typifies the clamp loader clade to which it belongs [1,68]. The DnaA AAA+ module from Aquifex aeolicus (left, PDB 2HCB2HCB) contains an insert of two equal-sized helices (pink) after the second β-strand and is representative of the initiation clade . The RuvB AAA+ module from T. thermophilus (right, PDB 1HQC) contains a β-hairpin insert (pink) between sensor 1 and its preceding helix . This insert is characteristic of the RuvB family and is known to be important for the interaction of RuvB with RuvA in the resolution of Holliday junctions in DNA recombination [69,70]. The function of RuvB is discussed in the text. (c) Representatives of the PACTT group. Members of this group all contain a β-hairpin insert (cyan, shown in all three structures) between the sensor 1 strand and the preceding helix . The BchI AAA+ module from Rhodobacter capsulatus Mg2+ chelatase (left, PDB 1G8P) belongs to the helix-2 insert clade. Members of this clade contain a small insert of two β-strands flanking a small α-helix (pink) in helix 2 of the αβα core domain and a long helical insert (yellow) between the fifth β-strand of the core domain and the small α-helical domain [1,24]. BchI proteins also contain a long, highly conserved β-hairpin insert (orange) upstream of the second β-strand of the core domain . The function of BchI is discussed in the text. The carboxy-terminal ClpA AAA+ module (D2) from Escherichia coli (center, PDB 1KSF)  and the HslU AAA+ module from E. coli (right, PDB 1G4A)  are both representative members of the HCL clade, whose members are involved in protein unfolding and degradation. These structures contain an extended loop (pink) between the second core β-strand and the following helix  and a two or three stranded β-sheet insert (yellow) in the small α-helical domain of the AAA+ module, both characteristic of this clade. In addition, HslU family members contain an additional 130 amino acid I domain (orange, only part of the domain is resolved in the crystal structure) inserted into the core αβα domain of the AAA+ module, which is proposed to play a role in substrate recognition and unfolding .
Snider et al. Genome Biology 2008 9:216 doi:10.1186/gb-2008-9-4-216