Cell Science at a Glance on the Web: electronic copies of the full-size poster insert are available in various formats Members of the AAA (for ATPases associated with various cellular activities) protein superfamily are characterized by the presence of one or two highly conserved modules of approximately 230 amino acid residues (the AAA box) that include an ATP-binding consensus. AAA proteins are found in all organisms and are essential for cell cycle functions, vesicular transport, mitochondrial functions, peroxisome assembly and proteolysis. This unrooted phylogenetic tree of the AAA superfamily is derived from an alignment of 345 AAA boxes from 316 AAA proteins in 92 species. For proteins (Table 1) with a duplicate AAA box, the more conserved box was used for tree construction (the N-terminal box of the secretion/neurotransmission proteins and the C-terminal box of the peroxisomal proteins). Because most members of the CDC48/homotypic-fusion family contain two well-conserved AAA boxes, both copies were included in the tree for these proteins. There are a few exceptions for which only one box was used (e.g. the C-terminal AAA boxes of Ce K04G2.3 and Myt MTCY22G10.32c and the N-terminal AAA boxes of Hs BAB14017.1 and Sc YTA7). I have omitted some sequences classified as AAA proteins by others - for example, AFG1 and BCS1 from Saccharomyces cerevisiae, and PRS2 from Methanococcus jannaschii. As is the case with many classifications, there is no clear-cut border between members of the AAA protein family and non-members. All AAA sequences used in this tree form a distinct cluster and clearly have shorter branches than any more-distant relatives. The protein sequences of the respective AAA boxes were aligned for optimal similarity, and the tree data were calculated by Clustal W with default settings (gaps not excluded, Blosum matrix). The tree was drawn with TreeView (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html). During further editing, some crossing branches were untangled, but the branch lengths or branching points were left unchanged*. The reliability of the tree was verified by bootstrapping (1000 trials) with Clustal W. Internal branches that occur in >80% of the bootstrap samples are marked by filled circles. Although most of the proposed families and subfamilies (e.g. the Pex1 and Pex6 proteasome subunits) are confirmed by the bootstrapping, the boundaries of the CDC48/homotypic-fusion family appear less well defined. The molecular cartoons illustrate the overall structure of some AAA proteins: proteins that have a duplicated AAA box form homohexameric rings (because the structure of the Pex proteins is still unclear, a monomer is shown as an alternative structure), as do the ARC family proteins; a ring of six different AAA proteins forms the base of the 19S lid on both sides of the proteasome core; the YTA10-YTA12 heterohexamer and YME1 homohexamer in the inner mitochondrial membrane have different orientations owing to the loss of a transmembrane domain in YME1. More information on the AAA proteins, including a search module and links to other databases can be found at the AAA Family Server (current address http://yeamob.pci.chemie.uni-tuebingen.de/AAA/ but please note that the AAA family server will move to AAA-proteins.uni-graz.ac.at in September, 2001). The complete alignment and bootstrapping data are available at http://yeamob.pci.chemie.uni-tuebingen.de/AAA/Poster/. *For practical reasons, the Pex/C-terminal-Cdc48 family cluster is derived from a separate calculation. For bootstrapping, the complete data set has been used.

• PMID: 11309190
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Fröhlich KU

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