8VES

Structure of YicC endoribonuclease bound to an RNA substrate

Summary for 8VES

• Entry DOI: 10.2210/pdb8ves/pdb
• EMDB information: 43173
• Descriptor: Endoribonuclease YicC, RNA (26-MER) (3 entities in total)
• Functional Keywords: endoribonuclease, hexamer, e. coli, hydrolase
• Biological source: Escherichia coli; More
• Total number of polymer chains: 7
• Total formula weight: 208667.39

Authors

Wu, R.,Lazarus, M.B. (deposition date: 2023-12-20, release date: 2024-09-04, Last modification date: 2024-10-09)

Primary citation

Wu, R.,Ingle, S.,Barnes, S.A.,Dahlin, H.R.,Khamrui, S.,Xiang, Y.,Shi, Y.,Bechhofer, D.H.,Lazarus, M.B.
Structural insights into RNA cleavage by a novel family of bacterial RNases.
Nucleic Acids Res., 52:10705-10716, 2024

PubMed Abstract: Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.

PubMed: 39180400
DOI: 10.1093/nar/gkae717

Experimental method

ELECTRON MICROSCOPY (3.22 Å)