6CGL

X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound as-isolated (pH 4)

6CGL の概要

• エントリーDOI: 10.2210/pdb6cgl/pdb
• 分子名称: Ribonucleoside-diphosphate reductase, 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: ribonucleotide reductase, allostery, nucleotide metabolism, oxidoreductase, damp
• 由来する生物種: Bacillus subtilis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 162725.70

構造登録者

Maggiolo, A.O.,Boal, A.K. (登録日: 2018-02-20, 公開日: 2018-05-09, 最終更新日: 2024-05-29)

主引用文献

Parker, M.J.,Maggiolo, A.O.,Thomas, W.C.,Kim, A.,Meisburger, S.P.,Ando, N.,Boal, A.K.,Stubbe, J.
An endogenous dAMP ligand inBacillus subtilisclass Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP.
Proc. Natl. Acad. Sci. U.S.A., 115:E4594-E4603, 2018

PubMed Abstract: The high fidelity of DNA replication and repair is attributable, in part, to the allosteric regulation of ribonucleotide reductases (RNRs) that maintains proper deoxynucleotide pool sizes and ratios in vivo. In class Ia RNRs, ATP (stimulatory) and dATP (inhibitory) regulate activity by binding to the ATP-cone domain at the N terminus of the large α subunit and altering the enzyme's quaternary structure. Class Ib RNRs, in contrast, have a partial cone domain and have generally been found to be insensitive to dATP inhibition. An exception is the Ib RNR, which we recently reported to be inhibited by physiological concentrations of dATP. Here, we demonstrate that the α subunit of this RNR contains tightly bound deoxyadenosine 5'-monophosphate (dAMP) in its N-terminal domain and that dATP inhibition of CDP reduction is enhanced by its presence. X-ray crystallography reveals a previously unobserved (noncanonical) α dimer with its entire interface composed of the partial N-terminal cone domains, each binding a dAMP molecule. Using small-angle X-ray scattering (SAXS), we show that this noncanonical α dimer is the predominant form of the dAMP-bound α in solution and further show that addition of dATP leads to the formation of larger oligomers. Based on this information, we propose a model to describe the mechanism by which the noncanonical α inhibits the activity of the Ib RNR in a dATP- and dAMP-dependent manner.

PubMed: 29712847
DOI: 10.1073/pnas.1800356115

実験手法

X-RAY DIFFRACTION (3.2 Å)