5EKB: R2-like ligand-binding oxidase with aerobically reconstituted Mn/Fe cofactor (reconstituted in solution)

A manganese/iron cofactor which performs multi-electron oxidative chemistry is found in two classes of ferritin-like proteins, the small subunit (R2) of class Ic ribonucleotide reductase (R2c) and the R2-like ligand-binding oxidase (R2lox). It is unclear how a heterodimeric Mn/Fe metallocofactor is assembled in these two related proteins as opposed to a homodimeric Fe/Fe cofactor, especially considering the structural similarity and proximity of the two metal-binding sites in both protein scaffolds and the similar first coordination sphere ligand preferences of Mn(II) and Fe(II). Using EPR and Mossbauer spectroscopies as well as X-ray anomalous dispersion, we examined metal loading and cofactor activation of both proteins in vitro (in solution). We find divergent cofactor assembly mechanisms for the two systems. In both cases, excess Mn(II) promotes heterobimetallic cofactor assembly. In the absence of Fe(II), R2c cooperatively binds Mn(II) at both metal sites, whereas R2lox does not readily bind Mn(II) at either site. Heterometallic cofactor assembly is favored at substoichiometric Fe(II) concentrations in R2lox. Fe(II) and Mn(II) likely bind to the protein in a stepwise fashion, with Fe(II) binding to site 2 initiating cofactor assembly. In R2c, however, heterometallic assembly is presumably achieved by the displacement of Mn(II) by Fe(II) at site 2. The divergent metal loading mechanisms are correlated with the putative in vivo functions of R2c and R2lox, and most likely with the intracellular Mn(II)/Fe(II) concentrations in the host organisms from which they were isolated.
PDB ID: 5EKBDownload
MMDB ID: 138538
PDB Deposition Date: 2015/11/3
Updated in MMDB: 2016/11
Experimental Method:
x-ray diffraction
Resolution: 2.074  Å
Source Organism:
Similar Structures:
Biological Unit for 5EKB: dimeric; determined by author and by software (PISA)
Molecular Components in 5EKB
Label Count Molecule
Proteins (2 molecules)
Ribonucleotide Reductase Small Subunit
Molecule annotation
Chemicals (6 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB