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PDBsum entry 5e71
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References listed in PDB file
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Key reference
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Title
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Structural and functional analyses of the archaeal tRNA m2g/m22g10 methyltransferase atrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-Binding modules.
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Authors
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A.Hirata,
S.Nishiyama,
T.Tamura,
A.Yamauchi,
H.Hori.
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Ref.
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Nucleic Acids Res, 2016,
44,
6377-6390.
[DOI no: ]
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PubMed id
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Abstract
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N(2)-methylguanosine is one of the most universal modified nucleosides required
for proper function in transfer RNA (tRNA) molecules. In archaeal tRNA species,
a specific S-adenosyl-L-methionine (SAM)-dependent tRNA methyltransferase
(MTase), aTrm11, catalyzes formation of N(2)-methylguanosine and
N(2),N(2)-dimethylguanosine at position 10. Here, we report the first X-ray
crystal structures of aTrm11 from Thermococcus kodakarensis (Tko), of the
apo-form, and of its complex with SAM. The structures show that TkoTrm11
consists of three domains: an N-terminal ferredoxinlike domain (NFLD), THUMP
domain and Rossmann-fold MTase (RFM) domain. A linker region connects the
THUMP-NFLD and RFM domains. One SAM molecule is bound in the pocket of the RFM
domain, suggesting that TkoTrm11 uses a catalytic mechanism similar to that of
other tRNA MTases containing an RFM domain. Furthermore, the conformation of
NFLD and THUMP domains in TkoTrm11 resembles that of other tRNA-modifying
enzymes specifically recognizing the tRNA acceptor stem. Our docking model of
TkoTrm11-SAM in complex with tRNA, combined with biochemical analyses and
pre-existing evidence, provides insights into the substrate tRNA recognition
mechanism: The THUMP domain recognizes a 3'-ACCA end, and the linker region and
RFM domain recognize the T-stem, acceptor stem and V-loop of tRNA, thereby
causing TkoTrm11 to specifically identify its methylation site.
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