8Z62
Crystal structure of rRNA (uracil-C5)-methyltransferase from Pyrococcus horikoshii OT3
Summary for 8Z62
| Entry DOI | 10.2210/pdb8z62/pdb |
| Descriptor | 23S rRNA (uracil(747)-C(5))-methyltransferase, SODIUM ION, SULFATE ION, ... (6 entities in total) |
| Functional Keywords | archaea, aromatic stacking, hinge movement, horizontal gene transfer, iron-sulfur protein, substrate selectivity, transferase |
| Biological source | Pyrococcus horikoshii OT3 |
| Total number of polymer chains | 2 |
| Total formula weight | 95276.15 |
| Authors | |
| Primary citation | Saha, S.,Kanaujia, S.P. Decoding Substrate Selectivity of an Archaeal RlmCD-like Methyltransferase Through Its Salient Traits. Biochemistry, 63:2477-2492, 2024 Cited by PubMed Abstract: 5-Methyluridine (mU) rRNA modifications frequently occur at U747 and U1939 ( numbering) in domains II and IV of the 23S rRNA in Gram-negative bacteria, with the help of -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 group, have been found to possess two genes encoding SAM-dependent archaeal (tRNA and rRNA) mU (ArmU) MTases. Among these, a tRNA-specific ArmU MTase (TrmU54) has already been characterized. This study focused on the structural and functional characterization of the rRNA-specific ArmU MTase from the hyperthermophilic archaeon (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 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 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 ArmU MTases originated from horizontal gene transfer events, most likely from Gram-positive bacteria. PubMed: 39350642DOI: 10.1021/acs.biochem.4c00401 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.2 Å) |
Structure validation
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