7PVM

NMR structure of the C. thermophilum Xrn2 zinc finger

Summary for 7PVM

• Entry DOI: 10.2210/pdb7pvm/pdb
• Related: 7OPK
• NMR Information: BMRB: 50997
• Descriptor: 5'-3' exoribonuclease, ZINC ION (2 entities in total)
• Functional Keywords: zinc finger, rna binding protein
• Biological source: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
• Total number of polymer chains: 1
• Total formula weight: 3376.22

Authors

Overbeck, J.H.,Sprangers, R.,Wurm, J.P. (deposition date: 2021-10-05, release date: 2022-07-06, Last modification date: 2024-06-19)

Primary citation

Overbeck, J.H.,Stelzig, D.,Fuchs, A.L.,Wurm, J.P.,Sprangers, R.
Observation of conformational changes that underlie the catalytic cycle of Xrn2.
Nat.Chem.Biol., 18:1152-1160, 2022

PubMed Abstract: Nuclear magnetic resonance (NMR) methods that quantitatively probe motions on molecular and atomic levels have propelled the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. In this work, we studied the structure and dynamics of the essential 100-kDa eukaryotic 5'→3' exoribonuclease Xrn2. A combination of complementary fluorine and methyl-TROSY NMR spectroscopy reveals that the apo enzyme is highly dynamic around the catalytic center. These observed dynamics are in agreement with a transition of the enzyme from the ground state into a catalytically competent state. We show that the conformational equilibrium in Xrn2 shifts substantially toward the active state in the presence of substrate and magnesium. Finally, our data reveal that the dynamics in Xrn2 correlate with the RNA degradation rate, as a mutation that attenuates motions also affects catalytic activity. In that light, our results stress the importance of studies that go beyond static structural information.

PubMed: 36008487
DOI: 10.1038/s41589-022-01111-6

Experimental method

SOLUTION NMR