Download MendeleyDecoding Substrate Selectivity of an Archaeal RlmCD-like Methyltransferase Through Its Salient Traits.
Saha, S., Kanaujia, S.P.(2024) Biochemistry 63: 2477-2492
- PubMed: 39350642
- DOI: https://doi.org/10.1021/acs.biochem.4c00401
- Primary Citation of Related Structures:
8Z62 - PubMed Abstract:
5-Methyluridine (m 5 U) rRNA modifications frequently occur at U747 and U1939 ( Escherichia coli numbering) in domains II and IV of the 23S rRNA in Gram-negative bacteria, with the help of S -adenosyl-l-methionine (SAM)-dependent rRNA methyltransferases (MTases), RlmC and RlmD, respectively. In contrast, Gram-positive bacteria utilize a single SAM-dependent rRNA MTase, RlmCD, to modify both corresponding sites. Notably, certain archaea, specifically within the Thermococcales group, have been found to possess two genes encoding SAM-dependent archaeal (tRNA and rRNA) m 5 U (Arm 5 U) MTases. Among these, a tRNA-specific Arm 5 U MTase ( Pab TrmU54) has already been characterized. This study focused on the structural and functional characterization of the rRNA-specific Arm 5 U MTase from the hyperthermophilic archaeon Pyrococcus horikoshii ( Ph RlmCD). An in-depth structural examination revealed a dynamic hinge movement induced by the replacement of the iron-sulfur cluster with disulfide bonds, obstructing the substrate-binding site. It revealed distinctive characteristics of Ph RlmCD, including elongated positively charged loops in the central domain and rotational variations in the TRAM domain, which influence substrate selectivity. Additionally, the results suggested that two potential mini-rRNA fragments interact in a similar manner with Ph RlmCD at a positively charged cleft at the interface of domains and facilitate dual MTase activities akin to the protein RlmCD. Altogether, these observations showed that Arm 5 U MTases originated from horizontal gene transfer events, most likely from Gram-positive bacteria.
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
Organizational Affiliation:
