Summary information and primary citation
- PDB-id
-
4yvk;
DSSR-derived features in text and
JSON formats; DNAproDB
- Class
- transferase-RNA
- Method
- X-ray (3.002 Å)
- Summary
- Crystal structure of h. influenzae trmd in complex with
sinefungin and trna variant (g36c)
- Reference
-
Ito T, Masuda I, Yoshida K, Goto-Ito S, Sekine S, Suh SW,
Hou YM, Yokoyama S (2015): "Structural
basis for methyl-donor-dependent and sequence-specific
binding to tRNA substrates by knotted methyltransferase
TrmD." Proc.Natl.Acad.Sci.USA,
112, E4197-E4205. doi: 10.1073/pnas.1422981112.
- Abstract
- The deep trefoil knot architecture is unique to the
SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of
methyltransferases (MTases) in all three domains of life.
In bacteria, TrmD catalyzes the N(1)-methylguanosine
(m(1)G) modification at position 37 in transfer RNAs
(tRNAs) with the (36)GG(37) sequence, using
S-adenosyl-l-methionine (AdoMet) as the methyl donor. The
m(1)G37-modified tRNA functions properly to prevent +1
frameshift errors on the ribosome. Here we report the
crystal structure of the TrmD homodimer in complex with a
substrate tRNA and an AdoMet analog. Our structural
analysis revealed the mechanism by which TrmD binds the
substrate tRNA in an AdoMet-dependent manner. The
trefoil-knot center, which is structurally conserved among
SPOUT MTases, accommodates the adenosine moiety of AdoMet
by loosening/retightening of the knot. The TrmD-specific
regions surrounding the trefoil knot recognize the
methionine moiety of AdoMet, and thereby establish the
entire TrmD structure for global interactions with tRNA and
sequential and specific accommodations of G37 and G36,
resulting in the synthesis of m(1)G37-tRNA.
