1YFD

Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli

Summary for 1YFD

• Entry DOI: 10.2210/pdb1yfd/pdb
• Related: 1BIQ 1MXR 1PFR 1PIM 1XIK
• Descriptor: Ribonucleoside-diphosphate reductase 1 beta chain, MERCURY (II) ION, MU-OXO-DIIRON, ... (4 entities in total)
• Functional Keywords: di-iron center, oxidoreductase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 89666.72

Authors

Kolberg, M.,Logan, D.T.,Bleifuss, G.,Poetsch, S.,Sjoeberg, B.M.,Graeslund, A.,Lubitz, W.,Lassmann, G.,Lendzian, F. (deposition date: 2004-12-31, release date: 2005-02-15, Last modification date: 2023-08-23)

Primary citation

Kolberg, M.,Logan, D.T.,Bleifuss, G.,Poetsch, S.,Sjoeberg, B.M.,Graeslund, A.,Lubitz, W.,Lassmann, G.,Lendzian, F.
A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies
J.Biol.Chem., 280:11233-11246, 2005

PubMed Abstract: The R2 protein subunit of class I ribonucleotide reductase (RNR) belongs to a structurally related family of oxygen bridged diiron proteins. In wild-type R2 of Escherichia coli, reductive cleavage of molecular oxygen by the diferrous iron center generates a radical on a nearby tyrosine residue (Tyr122), which is essential for the enzymatic activity of RNR, converting ribonucleotides into deoxyribonucleotides. In this work, we characterize the mutant E. coli protein R2-Y122H, where the radical site is substituted with a histidine residue. The x-ray structure verifies the mutation. R2-Y122H contains a novel stable paramagnetic center which we name H, and which we have previously proposed to be a diferric iron center with a strongly coupled radical, Fe(III)Fe(III)R.. Here we report a detailed characterization of center H, using 1H/2H -14N/15N- and 57Fe-ENDOR in comparison with the Fe(III)Fe(IV) intermediate X observed in the iron reconstitution reaction of R2. Specific deuterium labeling of phenylalanine residues reveals that the radical results from a phenylalanine. As Phe208 is the only phenylalanine in the ligand sphere of the iron site, and generation of a phenyl radical requires a very high oxidation potential, we propose that in Y122H residue Phe208 is hydroxylated, as observed earlier in another mutant (R2-Y122F/E238A), and further oxidized to a phenoxyl radical, which is coordinated to Fe1. This work demonstrates that small structural changes can redirect the reactivity of the diiron site, leading to oxygenation of a hydrocarbon, as observed in the structurally similar methane monoxygenase, and beyond, to formation of a stable iron-coordinated radical.

PubMed: 15634667
DOI: 10.1074/jbc.M414634200

Experimental method

X-RAY DIFFRACTION (1.9 Å)