5ZQ1

Crystal structure of spRlmCD with U1939loop RNA at 3.10 angstrom

Summary for 5ZQ1

• Entry DOI: 10.2210/pdb5zq1/pdb
• Related: 5XJ1
• Descriptor: Uncharacterized RNA methyltransferase SP_1029, RNA (5'-R(*AP*AP*AP*(MUM)P*UP*CP*CP*U)-3'), S-ADENOSYL-L-HOMOCYSTEINE (3 entities in total)
• Functional Keywords: methyltransferase, ribosome, 23s rna, streptococcus pneumoniae, transferase, transferase-rna complex, transferase/rna
• Biological source: Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4); More
• Total number of polymer chains: 2
• Total formula weight: 54027.81

Authors

Yu, H.L.,Jiang, Y.Y. (deposition date: 2018-04-17, release date: 2018-10-24, Last modification date: 2024-11-06)

Primary citation

Jiang, Y.,Yu, H.,Li, F.,Cheng, L.,Zhu, L.,Shi, Y.,Gong, Q.
Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD
PLoS Pathog., 14:e1007379-e1007379, 2018

PubMed Abstract: Methyltransferase RlmCD was previously shown to be responsible for the introduction of C5 methylation at both U747 and U1939 of the 23S ribosomal RNA in Streptococcus pneumoniae. Intriguingly, its structural homologue, RumA, can only catalyze the methylation of U1939, while RlmC is the dedicated enzyme for m5U747 in Escherichia coli. In this study, we describe the structure of RlmCD in complex with its cofactor and the RNA substrate containing U747 at 2.00 Å or U1939 at 3.10 Å. We demonstrate that multiple structural features collaborate to establish the dual enzymatic activities of RlmCD. Of them, the side-chain rearrangement of F145 was observed to be an unusual mechanism through which RlmCD can discriminate between U747- and U1939-containing RNA substrate by switching the intermolecular aromatic stacking between protein and RNA on/off. An in-vitro methyltransferase assay and electrophoretic mobility shift assay were performed to validate these findings. Overall, our complex structures allow for a better understanding of the dual-functional mechanism of RlmCD, suggesting useful implications for the evolution of the RumA-type enzyme and the potential development of antibiotic drugs against S. pneumoniae.

PubMed: 30388185
DOI: 10.1371/journal.ppat.1007379

Experimental method

X-RAY DIFFRACTION (3.1 Å)