5OLK

Crystal structure of the ATP-cone-containing NrdB from Leeuwenhoekiella blandensis

Summary for 5OLK

• Entry DOI: 10.2210/pdb5olk/pdb
• Descriptor: Ribonucleoside-diphosphate reductase, beta subunit 1, 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: ribonucleotide reductase atp cone allosteric regulation oligomerization, oxidoreductase
• Biological source: Leeuwenhoekiella blandensis (strain CECT 7118 / CCUG 51940 / MED217)
• Total number of polymer chains: 4
• Total formula weight: 204833.14

Authors

Hasan, M.,Grinberg, A.R.,Sjoberg, B.M.,Logan, D.T. (deposition date: 2017-07-28, release date: 2018-01-10, Last modification date: 2024-01-17)

Primary citation

Rozman Grinberg, I.,Lundin, D.,Hasan, M.,Crona, M.,Jonna, V.R.,Loderer, C.,Sahlin, M.,Markova, N.,Borovok, I.,Berggren, G.,Hofer, A.,Logan, D.T.,Sjoberg, B.M.
Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit.
Elife, 7:-, 2018

PubMed Abstract: Ribonucleotide reductases (RNRs) are key enzymes in DNA metabolism, with allosteric mechanisms controlling substrate specificity and overall activity. In RNRs, the activity master-switch, the ATP-cone, has been found exclusively in the catalytic subunit. In two class I RNR subclasses whose catalytic subunit lacks the ATP-cone, we discovered ATP-cones in the radical-generating subunit. The ATP-cone in the radical-generating subunit regulates activity via quaternary structure induced by binding of nucleotides. ATP induces enzymatically competent dimers, whereas dATP induces non-productive tetramers, resulting in different holoenzymes. The tetramer forms by interactions between ATP-cones, shown by a 2.45 Å crystal structure. We also present evidence for an MnMn metal center. In summary, lack of an ATP-cone domain in the catalytic subunit was compensated by transfer of the domain to the radical-generating subunit. To our knowledge, this represents the first observation of transfer of an allosteric domain between components of the same enzyme complex.

PubMed: 29388911
DOI: 10.7554/eLife.31529

Experimental method

X-RAY DIFFRACTION (2.45 Å)