The P-loop (see <PDOC00017>) guanosine triphosphatases (GTPases) control a multitude of biological processes, ranging from cell division, cell cycling, and signal transduction, to ribosome assembly and protein synthesis. GTPases exert their control by interchanging between an inactive GDP-bound state and an active GTP-bound state, thereby acting as molecular switches. The common denominator of GTPases is the highly conserved guanine nucleotide-binding (G) domain that is responsible for binding and hydrolysis of guanine nucleotides.

The TRAFAC (named after translation factors) class includes an atypical family characterized by a circularly permuted (CP) order of the GTPase motifs within the G domain: the normal G1-G2-G3-G4-G5 orientation of the G domain has been rearranged to G4(N/T-K-x-D)-G5(T/G-C/S-A)-G1(Walker A, P-loop)-G2(T)-G3(Walker B). Despite such a variation (in motif order) observed at the primary sequence level, which should lead to different topological connections between the secondary structure elements, the three dimensional fold is well preserved. In addition, the GTP-binding site too is well conserved. It has been proposed that the CP-type G domain has evolved due to the duplication of a classical GTPase domain followed by deletion of both N- and C-terminal regions. The CP-type G domain is unlikely to exist as a single domain and is accompanied by at least one additional domain [1,2,3].

The CP-type G domain has a typical G domain fold with a central seven-stranded β-sheet (six parallel strands, one antiparallel strand) surrounded by six α-helices (see <PDB:3EC1>) [3,4,5,6].

Some proteins known to contain a CP-type G domain are listed below:

• Bacterial YjeQ (RsgA), composed of a N-terminal oligonucleotide/ oligosaccharide binding (OB-fold) RNA-binding domain, a central G domain, and a C-terminal cysteine cluster forming a zinc-finger motif. YjeQ GTPases assist in ribosome biogenesis and bind to the 30S subunit of mature ribosomes [3,6].
• MTG1/YlqF from eukaryotes, archaea, and bacteria. It is involved in ribosome biogenesis [5].
• NOA1/MTG3/YqeH from eukaryotes and bacteria, binds ribosomes and consequently plays a role in their proper assembly and/or stability [4,7,8,9].
• Nug2/YawG subfamily GTPases from eukaryotes and bacteria, implicated in biogenesis of the 60S ribosomal subunit [10].

The profile we developed covers the entire CP-type G domain.