A radical S-adenosylmethionine enzyme caught in the act of modifying tRNA
Amy Boal and Squire Booker groups (Pennsylvania State University)
The groups of Amie Boal and Squire Booker at the
Pennsylvania State University determined the structure of the
dual-specificity RNA methylase, RlmN, cross-linked to a tRNA substrate.
RlmN, which is a member of the radical S-adenosylmethionine (SAM)
superfamily of enzymes, methylates both ribosomal and transfer RNAs at
the C2 position of specific adenine nucleotides using a unique radical
mechanism that involves a cross-linked protein/nucleic acid
intermediate. The methylation of A2503 in domain V of 23S rRNA has
been reported to enhance translational fidelity. By changing a key
cysteine residue to alanine, the groups were able to trap an RlmN-tRNA
cross-linked structure at this intermediate step and solve its
structure, giving insight into substrate recognition and several
unresolved details of the mechanism. The structure is the first view
of a dual-specificity methylase bound to a full-length RNA substrate.
RlmN forms an extended interface with tRNA, which is rare among
tRNA-modifying enzymes, but is similar to the binding mode of tRNA
synthetases; this provides an unusual induced-fit mechanism for binding
the tRNA, which completely disrupts the structure of the anticodon
stem-loop. The capacity to significantly remodel the substrate is
likely key in the ability of RlmN to target two different forms of RNA,
and is distinct from the only other known dual-specificity RNA
modifying enzyme, RluA. RlmN has a close evolutionary relationship and
enzymatic mechanism to Cfr, which methylates the C8 position of the
same nucleotide (A2503) in the same rRNA. In contrast to RlmN, Cfr
confers resistance to several different classes of clinically-used
antibiotics. The structure of RlmN in complex with an RNA substrate
could aid in structure-based design of new antibacterial agents
targeting Cfr.
 |
Figure: Cartoon diagram of
RNA-modifying enzyme RlmN (blue) bound to tRNA (gray). The
space-filling iron-sulfur cluster is colored by atom type. The
cross-link and SAM cleavage products are shown in stick format and are
colored by atom type. |
Citation: Schwalm, E.L., Grove, T.L., Booker,
S.J., and Boal, A.K. (2016) Crystallographic capture of a
radical S-adenosylmethionine enzyme in the act of modifying tRNA.
Science 352, 309-312.
|