2XO5: Ribonucleotide Reductase Y731nh2y Modified R1 Subunit Of E. Coli

Citation:
Abstract
Escherichia coli ribonucleotide reductase is an alpha2beta2 complex and catalyzes the conversion of nucleoside 5'-diphosphates (NDPs) to 2'-deoxynucleotides (dNDPs). The reaction is initiated by the transient oxidation of an active-site cysteine (C(439)) in alpha2 by a stable diferric tyrosyl radical (Y(122)*) cofactor in beta2. This oxidation occurs by a mechanism of long-range proton-coupled electron transfer (PCET) over 35 A through a specific pathway of residues: Y(122)*--> W(48)--> Y(356) in beta2 to Y(731)--> Y(730)--> C(439) in alpha2. To study the details of this process, 3-aminotyrosine (NH(2)Y) has been site-specifically incorporated in place of Y(356) of beta. The resulting protein, Y(356)NH(2)Y-beta2, and the previously generated proteins Y(731)NH(2)Y-alpha2 and Y(730)NH(2)Y-alpha2 (NH(2)Y-RNRs) are shown to catalyze dNDP production in the presence of the second subunit, substrate (S), and allosteric effector (E) with turnover numbers of 0.2-0.7 s(-1). Evidence acquired by three different methods indicates that the catalytic activity is inherent to NH(2)Y-RNRs and not the result of copurifying wt enzyme. The kinetics of formation of 3-aminotyrosyl radical (NH(2)Y*) at position 356, 731, and 730 have been measured with all S/E pairs. In all cases, NH(2)Y* formation is biphasic (k(fast) of 9-46 s(-1) and k(slow) of 1.5-5.0 s(-1)) and kinetically competent to be an intermediate in nucleotide reduction. The slow phase is proposed to report on the conformational gating of NH(2)Y* formation, while the k(cat) of ~0.5 s(-1) is proposed to be associated with rate-limiting oxidation by NH(2)Y* of the subsequent amino acid on the pathway during forward PCET. The X-ray crystal structures of Y(730)NH(2)Y-alpha2 and Y(731)NH(2)Y-alpha2 have been solved and indicate minimal structural changes relative to wt-alpha2. From the data, a kinetic model for PCET along the radical propagation pathway is proposed.
PDB ID: 2XO5Download
MMDB ID: 84122
PDB Deposition Date: 2010/8/9
Updated in MMDB: 2012/10
Experimental Method:
x-ray diffraction
Resolution: 2.7  Å
Source Organism:
Escherichia coli K-12
Similar Structures:
Biological Unit for 2XO5: dodecameric; determined by software (PISA)
Molecular Components in 2XO5
Label Count Molecule
Proteins (12 molecules)
6
Ribonucleoside-diphosphate Reductase 1 Subunit Alpha(Gene symbol: nrdA)
Molecule annotation
6
Ribonucleoside-diphosphate Reductase 1 Subunit Beta(Gene symbol: nrdB)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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