7MZV

Structure of yeast pseudouridine synthase 7 (PUS7)

Summary for 7MZV

• Entry DOI: 10.2210/pdb7mzv/pdb
• Descriptor: Multisubstrate pseudouridine synthase 7, SULFATE ION (3 entities in total)
• Functional Keywords: pus7, pseudouridine synthase, rna binding protein, rbp, mrna modification, pseudouridine, isomerase
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Total number of polymer chains: 1
• Total formula weight: 78199.74

Authors

Purchal, M.,Koutmos, M. (deposition date: 2021-05-24, release date: 2022-02-09, Last modification date: 2024-10-09)

Primary citation

Purchal, M.K.,Eyler, D.E.,Tardu, M.,Franco, M.K.,Korn, M.M.,Khan, T.,McNassor, R.,Giles, R.,Lev, K.,Sharma, H.,Monroe, J.,Mallik, L.,Koutmos, M.,Koutmou, K.S.
Pseudouridine synthase 7 is an opportunistic enzyme that binds and modifies substrates with diverse sequences and structures.
Proc.Natl.Acad.Sci.USA, 119:-, 2022

PubMed Abstract: Pseudouridine (Ψ) is a ubiquitous RNA modification incorporated by pseudouridine synthase (Pus) enzymes into hundreds of noncoding and protein-coding RNA substrates. Here, we determined the contributions of substrate structure and protein sequence to binding and catalysis by pseudouridine synthase 7 (Pus7), one of the principal messenger RNA (mRNA) modifying enzymes. Pus7 is distinct among the eukaryotic Pus proteins because it modifies a wider variety of substrates and shares limited homology with other Pus family members. We solved the crystal structure of Pus7, detailing the architecture of the eukaryotic-specific insertions thought to be responsible for the expanded substrate scope of Pus7. Additionally, we identified an insertion domain in the protein that fine-tunes Pus7 activity both in vitro and in cells. These data demonstrate that Pus7 preferentially binds substrates possessing the previously identified UGAR (R = purine) consensus sequence and that RNA secondary structure is not a strong requirement for Pus7-binding. In contrast, the rate constants and extent of Ψ incorporation are more influenced by RNA structure, with Pus7 modifying UGAR sequences in less-structured contexts more efficiently both in vitro and in cells. Although less-structured substrates were preferred, Pus7 fully modified every transfer RNA, mRNA, and nonnatural RNA containing the consensus recognition sequence that we tested. Our findings suggest that Pus7 is a promiscuous enzyme and lead us to propose that factors beyond inherent enzyme properties (e.g., enzyme localization, RNA structure, and competition with other RNA-binding proteins) largely dictate Pus7 substrate selection.

PubMed: 35058356
DOI: 10.1073/pnas.2109708119

Experimental method

X-RAY DIFFRACTION (3.2 Å)