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

Authors
  • Rozman Grinberg, Inna1
  • Berglund, Sigrid2
  • Hasan, Mahmudul3
  • Lundin, Daniel1
  • Ho, Felix M2
  • Magnuson, Ann2
  • Logan, Derek T4
  • Sjöberg, Britt-Marie5
  • Berggren, Gustav6
  • 1 Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. , (Sweden)
  • 2 Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden. , (Sweden)
  • 3 Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden. , (Sweden)
  • 4 Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden. [email protected] , (Sweden)
  • 5 Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. [email protected] , (Sweden)
  • 6 Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden. [email protected] , (Sweden)
Type
Published Article
Journal
JBIC Journal of Biological Inorganic Chemistry
Publisher
Springer-Verlag
Publication Date
Sep 01, 2019
Volume
24
Issue
6
Pages
863–877
Identifiers
DOI: 10.1007/s00775-019-01697-8
PMID: 31414238
Source
Medline
Keywords
Language
English
License
Unknown

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 (O 2 ·- ). Considering the observed differences in the efficiency of these two activating reagents, we propose that the physiologically relevant mechanism involves superoxide.

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