5D0B

Crystal structure of epoxyqueuosine reductase with a tRNA-TYR epoxyqueuosine-modified tRNA stem loop

Summary for 5D0B

• Entry DOI: 10.2210/pdb5d0b/pdb
• Related: 5D08 5D0A
• Descriptor: Epoxyqueuosine reductase, RNA (5'-D(*GP*CP*AP*GP*AP*CP*UP*(56B)P*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'), IRON/SULFUR CLUSTER, ... (7 entities in total)
• Functional Keywords: b12, trna modification, heat-domain, queuosine, oxidoreductase-rna complex, oxidoreductase/rna
• Biological source: Bacillus subtilis (strain 168); More
• Total number of polymer chains: 3
• Total formula weight: 107376.03

Authors

Dowling, D.P.,Miles, Z.D.,Kohrer, C.,Bandarian, V.,Drennan, C.L. (deposition date: 2015-08-03, release date: 2016-09-28, Last modification date: 2023-09-27)

Primary citation

Dowling, D.P.,Miles, Z.D.,Kohrer, C.,Maiocco, S.J.,Elliott, S.J.,Bandarian, V.,Drennan, C.L.
Molecular basis of cobalamin-dependent RNA modification.
Nucleic Acids Res., 44:9965-9976, 2016

PubMed Abstract: Queuosine (Q) was discovered in the wobble position of a transfer RNA (tRNA) 47 years ago, yet the final biosynthetic enzyme responsible for Q-maturation, epoxyqueuosine (oQ) reductase (QueG), was only recently identified. QueG is a cobalamin (Cbl)-dependent, [4Fe-4S] cluster-containing protein that produces the hypermodified nucleoside Q in situ on four tRNAs. To understand how QueG is able to perform epoxide reduction, an unprecedented reaction for a Cbl-dependent enzyme, we have determined a series of high resolution structures of QueG from Bacillus subtilis Our structure of QueG bound to a tRNA anticodon stem loop shows how this enzyme uses a HEAT-like domain to recognize the appropriate anticodons and position the hypermodified nucleoside into the enzyme active site. We find Q bound directly above the Cbl, consistent with a reaction mechanism that involves the formation of a covalent Cbl-tRNA intermediate. Using protein film electrochemistry, we show that two [4Fe-4S] clusters adjacent to the Cbl have redox potentials in the range expected for Cbl reduction, suggesting how Cbl can be activated for nucleophilic attack on oQ. Together, these structural and electrochemical data inform our understanding of Cbl dependent nucleic acid modification.

PubMed: 27638883
DOI: 10.1093/nar/gkw806

Experimental method

X-RAY DIFFRACTION (2.645 Å)