6PGL

Structure of Kluyveromyces marxianus Usb1 with uridine monophosphate

Summary for 6PGL

• Entry DOI: 10.2210/pdb6pgl/pdb
• Descriptor: Uncharacterized protein YLR132C, GLYCEROL, URIDINE-5'-MONOPHOSPHATE, ... (8 entities in total)
• Functional Keywords: exonuclease, u6 snrna, 2h phosphodiesterase superfamily, hydrolase
• Biological source: Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275) (Yeast)
• Total number of polymer chains: 3
• Total formula weight: 76442.13

Authors

Nomura, Y.,Montemayor, E.J.,Butcher, S.E. (deposition date: 2019-06-24, release date: 2019-12-11, Last modification date: 2024-03-13)

Primary citation

Nomura, Y.,Montemayor, E.J.,Virta, J.M.,Hayes, S.M.,Butcher, S.E.
Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.
Nucleic Acids Res., 48:1423-1434, 2020

PubMed Abstract: U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2-8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n - 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.

PubMed: 31832688
DOI: 10.1093/nar/gkz1177

Experimental method

X-RAY DIFFRACTION (1.845 Å)