6SF5

Mn-containing form of the ribonucleotide reductase NrdB protein from Leeuwenhoekiella blandensis

Summary for 6SF5

• Entry DOI: 10.2210/pdb6sf5/pdb
• Related: 6SF4
• Descriptor: Ribonucleoside-diphosphate reductase, beta subunit 1, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: ribonucleotide reductase apoprotein manganese binding redox protein deoxyribonucleotide synthesis, metal binding protein
• Biological source: Leeuwenhoekiella blandensis
• Total number of polymer chains: 2
• Total formula weight: 81375.56

Authors

Hasan, M.,Rozman Grinberg, I.,Sjoberg, B.M.,Logan, D.T. (deposition date: 2019-08-01, release date: 2019-08-28, Last modification date: 2024-01-24)

Primary citation

Rozman Grinberg, I.,Berglund, S.,Hasan, M.,Lundin, D.,Ho, F.M.,Magnuson, A.,Logan, D.T.,Sjoberg, B.M.,Berggren, G.
Class Id ribonucleotide reductase utilizes a Mn2(IV,III) cofactor and undergoes large conformational changes on metal loading.
J.Biol.Inorg.Chem., 24:863-877, 2019

PubMed 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 Mn(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 Mn(IV,III) cofactor in class Id NrdB from Facklamia ignava. Once formed, the Mn(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. HO and superoxide (O ). Considering the observed differences in the efficiency of these two activating reagents, we propose that the physiologically relevant mechanism involves superoxide.

PubMed: 31414238
DOI: 10.1007/s00775-019-01697-8

Experimental method

X-RAY DIFFRACTION (1.9 Å)