PROSITE documentation PDOC51721Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile
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.
Last update:May 2020 / Profile revised.
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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Leipe D.D. Wolf Y.I. Koonin E.V. Aravind L. |
| Title | Classification and evolution of P-loop GTPases and related ATPases. | |
| Source | J. Mol. Biol. 317:41-72(2002). | |
| PubMed ID | 11916378 | |
| DOI | 10.1006/jmbi.2001.5378 |
| 2 | Authors | Anand B. Verma S.K. Prakash B. |
| Title | Structural stabilization of GTP-binding domains in circularly permuted GTPases: implications for RNA binding. | |
| Source | Nucleic Acids Res. 34:2196-2205(2006). | |
| PubMed ID | 16648363 | |
| DOI | 10.1093/nar/gkl178 |
| 3 | Authors | Shin D.H. Lou Y. Jancarik J. Yokota H. Kim R. Kim S.-H. |
| Title | Crystal structure of YjeQ from Thermotoga maritima contains a circularly permuted GTPase domain. | |
| Source | Proc. Natl. Acad. Sci. U.S.A. 101:13198-13203(2004). | |
| PubMed ID | 15331784 | |
| DOI | 10.1073/pnas.0405202101 |
| 4 | Authors | Sudhamsu J. Lee G.I. Klessig D.F. Crane B.R. |
| Title | The structure of YqeH. An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition. | |
| Source | J. Biol. Chem. 283:32968-32976(2008). | |
| PubMed ID | 18801747 | |
| DOI | 10.1074/jbc.M804837200 |
| 5 | Authors | Kim do J. Jang J.Y. Yoon H.-J. Suh S.W. |
| Title | Crystal structure of YlqF, a circularly permuted GTPase: implications for its GTPase activation in 50 S ribosomal subunit assembly. | |
| Source | Proteins 72:1363-1370(2008). | |
| PubMed ID | 18536017 | |
| DOI | 10.1002/prot.22112 |
| 6 | Authors | Nichols C.E. Johnson C. Lamb H.K. Lockyer M. Charles I.G. Hawkins A.R. Stammers D.K. |
| Title | Structure of the ribosomal interacting GTPase YjeQ from the enterobacterial species Salmonella typhimurium. | |
| Source | Acta Crystallogr. F 63:922-928(2007). | |
| PubMed ID | 18007041 | |
| DOI | 10.1107/S1744309107048609 |
| 7 | Authors | Moreau M. Lee G.I. Wang Y. Crane B.R. Klessig D.F. |
| Title | AtNOS/AtNOA1 is a functional Arabidopsis thaliana cGTPase and not a nitric-oxide synthase. | |
| Source | J. Biol. Chem. 283:32957-32967(2008). | |
| PubMed ID | 18801746 | |
| DOI | 10.1074/jbc.M804838200 |
| 8 | Authors | Liu H. Lau E. Lam M.P.Y. Chu H. Li S. Huang G. Guo P. Wang J. Jiang L. Chu I.K. Lo C. Tao Y. |
| Title | OsNOA1/RIF1 is a functional homolog of AtNOA1/RIF1: implication for a highly conserved plant cGTPase essential for chloroplast function. | |
| Source | New Phytol. 187:83-105(2010). | |
| PubMed ID | 20456051 | |
| DOI | 10.1111/j.1469-8137.2010.03264.x |
| 9 | Authors | Paul M.-F. Alushin G.M. Barros M.H. Rak M. Tzagoloff A. |
| Title | The putative GTPase encoded by MTG3 functions in a novel pathway for regulating assembly of the small subunit of yeast mitochondrial ribosomes. | |
| Source | J. Biol. Chem. 287:24346-24355(2012). | |
| PubMed ID | 22621929 | |
| DOI | 10.1074/jbc.M112.363309 |
| 10 | Authors | Im C.H. Hwang S.M. Son Y.S. Heo J.B. Bang W.Y. Suwastika I.N. Shiina T. Bahk J.D. |
| Title | Nuclear/nucleolar GTPase 2 proteins as a subfamily of YlqF/YawG GTPases function in pre-60S ribosomal subunit maturation of mono- and dicotyledonous plants. | |
| Source | J. Biol. Chem. 286:8620-8632(2011). | |
| PubMed ID | 21205822 | |
| DOI | 10.1074/jbc.M110.200816 |
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