Class Id ribonucleotide reductase utilizes a Mn2(IV,III) cofactor and undergoes large conformational changes on metal loading

Research output: Contribution to journalArticle

Abstract

Outside of the photosynthetic machinery, high-valent manganese cofactors are rare in biology. It was proposed that a recently discovered subclass of ribonucleotide reductase (RNR), class Id, is dependent on a Mn2(IV,III) cofactor for catalysis. Class I RNRs consist of a substrate-binding component (NrdA) and a metal-containing radical-generating component (NrdB). Herein we utilize a combination of EPR spectroscopy and enzyme assays to underscore the enzymatic relevance of the Mn2(IV,III) cofactor in class Id NrdB from Facklamia ignava. Once formed, the Mn2(IV,III) cofactor confers enzyme activity that correlates well with cofactor quantity. Moreover, we present the X-ray structure of the apo- and aerobically Mn-loaded forms of the homologous class Id NrdB from Leeuwenhoekiella blandensis, revealing a dimanganese centre typical of the subclass, with a tyrosine residue maintained at distance from the metal centre and a lysine residue projected towards the metals. Structural comparison of the apo- and metal-loaded forms of the protein reveals a refolding of the loop containing the conserved lysine and an unusual shift in the orientation of helices within a monomer, leading to the opening of a channel towards the metal site. Such major conformational changes have not been observed in NrdB proteins before. Finally, in vitro reconstitution experiments reveal that the high-valent manganese cofactor is not formed spontaneously from oxygen, but can be generated from at least two different reduced oxygen species, i.e. H2O2 and superoxide (O2 ·−). Considering the observed differences in the efficiency of these two activating reagents, we propose that the physiologically relevant mechanism involves superoxide.

Details

Authors
  • Inna Rozman Grinberg
  • Sigrid Berglund
  • Mahmudul Hasan
  • Daniel Lundin
  • Felix M. Ho
  • Ann Magnuson
  • Derek T. Logan
  • Britt Marie Sjöberg
  • Gustav Berggren
Organisations
External organisations
  • Stockholm University
  • Uppsala University
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Structural Biology

Keywords

  • Dimanganese cofactor, Electron paramagnetic resonance, Phylogeny, Radicals, Ribonucleotide reductase, X-ray crystallography
Original languageEnglish
Pages (from-to)863-877
JournalJournal of Biological Inorganic Chemistry
Volume24
Issue number6
Early online date2019
Publication statusPublished - 2019
Publication categoryResearch
Peer-reviewedYes