5WS2

Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus psychrophilus R15, complex with RNA

Summary for 5WS2

• Entry DOI: 10.2210/pdb5ws2/pdb
• Descriptor: Ribonuclease J, RNA (5'-R(P*AP*AP*AP*AP*A)-3'), ZINC ION, ... (5 entities in total)
• Functional Keywords: exoribonuclease, beta-casp, mbl, hydrolase
• Biological source: Methanolobus psychrophilus R15; More
• Cellular location: Cytoplasm : K4MAF9
• Total number of polymer chains: 4
• Total formula weight: 108657.25

Authors

Li, D.F.,Feng, N. (deposition date: 2016-12-05, release date: 2017-12-06, Last modification date: 2023-11-08)

Primary citation

Zheng, X.,Feng, N.,Li, D.,Dong, X.,Li, J.
New molecular insights into an archaeal RNase J reveal a conserved processive exoribonucleolysis mechanism of the RNase J family
Mol. Microbiol., 106:351-366, 2017

PubMed Abstract: RNase J, a prokaryotic 5'-3' exo/endoribonuclease, contributes to mRNA decay, rRNA maturation and post-transcriptional regulation. Yet the processive-exoribonucleolysis mechanism remains obscure. Here, we solved the first RNA-free and RNA-bound structures of an archaeal RNase J, and through intensive biochemical studies provided detailed mechanistic insights into the catalysis and processivity. Distinct dimerization/tetramerization patterns were observed for archaeal and bacterial RNase Js, and unique archaeal Loops I and II were found involved in RNA interaction. A hydrogen-bond-network was identified for the first time that assists catalysis by facilitating efficient proton transfer in the catalytic center. A conserved 5'-monophosphate-binding pocket that coordinates the RNA 5'-end ensures the 5'-monophosphate preferential exoribonucleolysis. To achieve exoribonucleolytic processivity, the 5'-monophosphate-binding pocket and nucleotide +4 binding site anchor RNA within the catalytic track; the 5'-capping residue Leu37 of the sandwich pocket coupled with the 5'-monophosphate-binding pocket are dedicated to translocating and controlling the RNA orientation for each exoribonucleolytic cycle. The processive-exoribonucleolysis mechanism was verified as conserved in bacterial RNase J and also exposes striking parallels with the non-homologous eukaryotic 5'-3' exoribonuclease, Xrn1. The findings in this work shed light on not only the molecular mechanism of the RNase J family, but also the evolutionary convergence of divergent exoribonucleases.

PubMed: 28795788
DOI: 10.1111/mmi.13769

Experimental method

X-RAY DIFFRACTION (2.398 Å)