5D1Y

Low resolution crystal structure of human ribonucleotide reductase alpha6 hexamer in complex with dATP

Summary for 5D1Y

• Entry DOI: 10.2210/pdb5d1y/pdb
• Descriptor: Ribonucleoside-diphosphate reductase large subunit (1 entity in total)
• Functional Keywords: deoxyribonucleotide, oligomerization, atp cone, oxidoreductase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 184700.78

Authors

Ando, N.,Li, H.,Brignole, E.J.,Thompson, S.,McLaughlin, M.I.,Page, J.,Asturias, F.,Stubbe, J.,Drennan, C.L. (deposition date: 2015-08-04, release date: 2016-01-20, Last modification date: 2024-10-09)

Primary citation

Ando, N.,Li, H.,Brignole, E.J.,Thompson, S.,McLaughlin, M.I.,Page, J.E.,Asturias, F.J.,Stubbe, J.,Drennan, C.L.
Allosteric Inhibition of Human Ribonucleotide Reductase by dATP Entails the Stabilization of a Hexamer.
Biochemistry, 55:373-381, 2016

PubMed Abstract: Ribonucleotide reductases (RNRs) are responsible for all de novo biosynthesis of DNA precursors in nature by catalyzing the conversion of ribonucleotides to deoxyribonucleotides. Because of its essential role in cell division, human RNR is a target for a number of anticancer drugs in clinical use. Like other class Ia RNRs, human RNR requires both a radical-generation subunit (β) and nucleotide-binding subunit (α) for activity. Because of their complex dependence on allosteric effectors, however, the active and inactive quaternary forms of many class Ia RNRs have remained in question. Here, we present an X-ray crystal structure of the human α subunit in the presence of inhibiting levels of dATP, depicting a ring-shaped hexamer (α6) where the active sites line the inner hole. Surprisingly, our small-angle X-ray scattering (SAXS) results indicate that human α forms a similar hexamer in the presence of ATP, an activating effector. In both cases, α6 is assembled from dimers (α2) without a previously proposed tetramer intermediate (α4). However, we show with SAXS and electron microscopy that at millimolar ATP, the ATP-induced α6 can further interconvert with higher-order filaments. Differences in the dATP- and ATP-induced α6 were further examined by SAXS in the presence of the β subunit and by activity assays as a function of ATP or dATP. Together, these results suggest that dATP-induced α6 is more stable than the ATP-induced α6 and that stabilization of this ring-shaped configuration provides a mechanism to prevent access of the β subunit to the active site of α.

PubMed: 26727048
DOI: 10.1021/acs.biochem.5b01207

Experimental method

X-RAY DIFFRACTION (9.005 Å)