7B9Q

The SERp optimized structure of Ribonucleotide reductase from Rhodobacter sphaeroides

Summary for 7B9Q

• Entry DOI: 10.2210/pdb7b9q/pdb
• Descriptor: Vitamin B12-dependent ribonucleotide reductase, 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: ribonucleotide reductase, thiyl radical enzyme, allosteric effector, oxidoreductase
• Biological source: Rhodobacter sphaeroides
• Total number of polymer chains: 2
• Total formula weight: 201727.35

Authors

Loderer, C.,Feiler, C.,Wilk, P.,Kabinger, F. (deposition date: 2020-12-14, release date: 2022-01-12, Last modification date: 2024-01-31)

Primary citation

Fietze, T.,Wilk, P.,Kabinger, F.,Anoosheh, S.,Hofer, A.,Lundin, D.,Feiler, C.G.,Weiss, M.S.,Loderer, C.
HUG Domain Is Responsible for Active Dimer Stabilization in an NrdJd Ribonucleotide Reductase.
Biochemistry, 61:1633-1641, 2022

PubMed Abstract: Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides. The catalytic activity of most RNRs depends on the formation of a dimer of the catalytic subunits. The active site is located at the interface, and part of the substrate binding site and regulatory mechanisms work across the subunit in the dimer. In this study, we describe and characterize a novel domain responsible for forming the catalytic dimer in several class II RNRs. The 3D structure of the class II RNR from reveals a so far undescribed α-helical domain in the dimer interface, which is embracing the other subunit. Genetic removal of this HUG domain leads to a severe reduction of activity paired with reduced dimerization capability. In comparison with other described RNRs, the enzyme with this domain is less dependent on the presence of nucleotides to act as allosteric effectors in the formation of dimers. The HUG domain appears to serve as an interlock to keep the dimer intact and functional even at low enzyme and/or effector concentrations.

PubMed: 35856337
DOI: 10.1021/acs.biochem.2c00173

Experimental method

X-RAY DIFFRACTION (2.78 Å)