Deciphering the catalytic machinery in 30S ribosome assembly GTPase YqeH
| Autor: | B Anand, Parag Surana, Balaji Prakash |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2010 |
| Předmět: |
GTP'
Computational Biology/Macromolecular Structure Analysis lcsh:Medicine Ribosome Subunits Small Bacterial Biochemistry/Biocatalysis GTPase Guanosine triphosphate Biology Catalysis Ribosome assembly GTP Phosphohydrolases 03 medical and health sciences chemistry.chemical_compound Computational Biology/Protein Homology Detection Biochemistry/Protein Chemistry 30S Homology modeling Biochemistry/Macromolecular Chemistry lcsh:Science Biochemistry/Biomacromolecule-Ligand Interactions 030304 developmental biology 0303 health sciences Aspartic Acid Multidisciplinary Sequence Homology Amino Acid Hydrolysis 030302 biochemistry & molecular biology lcsh:R Computational Biology/Macromolecular Sequence Analysis Circular permutation in proteins Biochemistry chemistry Biochemistry/Bioinformatics Computational Biology/Sequence Motif Analysis Biophysics Potassium lcsh:Q Guanosine Triphosphate Bacillus subtilis Research Article |
| Zdroj: | PLoS ONE, Vol 5, Iss 4, p e9944 (2010) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | Background YqeH, a circularly permuted GTPase (cpGTPase), which is conserved across bacteria and eukaryotes including humans is important for the maturation of small (30S) ribosomal subunit in Bacillus subtilis. Recently, we have shown that it binds 30S in a GTP/GDP dependent fashion. However, the catalytic machinery employed to hydrolyze GTP is not recognized for any of the cpGTPases, including YqeH. This is because they possess a hydrophobic substitution in place of a catalytic glutamine (present in Ras-like GTPases). Such GTPases were categorized as HAS-GTPases and were proposed to follow a catalytic mechanism, different from the Ras-like proteins. Methodology/principal findings MnmE, another HAS-GTPase, but not circularly permuted, utilizes a potassium ion and water mediated interactions to drive GTP hydrolysis. Though the G-domain of MnmE and YqeH share only approximately 25% sequence identity, the conservation of characteristic sequence motifs between them prompted us to probe GTP hydrolysis machinery in YqeH, by employing homology modeling in conjunction with biochemical experiments. Here, we show that YqeH too, uses a potassium ion to drive GTP hydrolysis and stabilize the transition state. However, unlike MnmE, it does not dimerize in the transition state, suggesting alternative ways to stabilize switches I and II. Furthermore, we identify a potential catalytic residue in Asp-57, whose recognition, in the absence of structural information, was non-trivial due to the circular permutation in YqeH. Interestingly, when compared with MnmE, helix alpha2 that presents Asp-57 is relocated towards the N-terminus in YqeH. An analysis of the YqeH homology model, suggests that despite such relocation, Asp-57 may facilitate water mediated catalysis, similarly as the catalytic Glu-282 of MnmE. Indeed, an abolished catalysis by D57I mutant supports this inference. Conclusions/significance An uncommon means to achieve GTP hydrolysis utilizing a K(+) ion has so far been demonstrated only for MnmE. Here, we show that YqeH also utilizes a similar mechanism. While the catalytic machinery is similar in both, mechanistic differences may arise based on the way they are deployed. It appears that K(+) driven mechanism emerges as an alternative theme to stabilize the transition state and hydrolyze GTP in a subset of GTPases, such as the HAS-GTPases. |
| Databáze: | OpenAIRE |
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