3MJO: Small subunit (R2F) of native ribonucleotide reductase from Corynebacterium ammoniagenes

Citation:
Abstract
The X-ray crystallographic structure of the native R2F subunit of the ribonucleotide reductase (RNR) of Corynebacterium ammoniagenes ATCC 6872 is reported, with a resolution of 1.36 A. The metal site contains an oxo/hydroxo-bridged manganese dimer, located near a tyrosine residue (Y115). The coordination of the manganese dimer and its distance to a nearby tyrosine residue resemble the di-iron metalloradical cofactor of class I RNR from Escherichia coli . Multifrequency EPR measurements of the highly active C. ammoniagenes R2F subunit show that the metal site contains a ferromagnetically exchange-coupled Mn(III)Mn(III) dimer weakly coupled to a tyrosyl radical. A mechanism for the metalloradical cofactor (Mn(III)Mn(III)Y(*)) generation is proposed. H(2)O(2) (HO(2)(-)) instead of O(2) is hypothesized as physiological oxidant for the Mn dimer which in turn oxidizes the tyrosine Y115. Changes in the ligand sphere of both manganese ions during metalloradical generation direct the complex formation of this cofactor, disfavoring alternate reaction pathways such as H(2)O(2) dismutation, as observed for manganese catalase, a structural analogue of the R2F metal site. The presented results demonstrate the importance of manganese for radical formation in this RNR and confirm the assignment of this enzyme to class Ib.
PDB ID: 3MJODownload
MMDB ID: 84387
PDB Deposition Date: 2010/4/13
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.36  Å
Source Organism:
Similar Structures:
Biological Unit for 3MJO: dimeric; determined by author and by software (PISA)
Molecular Components in 3MJO
Label Count Molecule
Proteins (2 molecules)
2
Ribonucleotide Reductase Subunit R2F
Molecule annotation
Chemicals (4 molecules)
1
4
* Click molecule labels to explore molecular sequence information.

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