Density Functional Theory Study of the Manganese-Containing Ribonucleotide Reductase from Chlamydia trachomatis: Why Manganese Is Needed in the Active Complex

Abstract

The active center of Chlamydia trachomatis (Ct) ribonucleotide reductase (RNR) has been studied using B3LYP hybrid density functional theory. Class Ic Ct RNR lacks the radical-bearing tyrosine that is crucial for activity in conventional class I (subclass a and b) RNR. Instead of the Fe(III)Fe(III)Tyr(rad) active state in conventional class I, Ct RNR has Mn(IV)Fe(III) at the metal center of subunit II. Based on calculated (H(+), e(-))-binding energies for Ct R2, iron-substituted Ct R2, and R2 from Escherichia coli (Ec), an explanation is proposed for why the enzyme needs this novel metal center. Mn(IV) is shown to be an equally strong oxidant as the tyrosyl radical in Ec R2. Fe(IV), however, is a much too strong oxidant and would therefore not be possible in the active cofactor. The structure of the catalytic center of the active state, such as protonation state and position of Mn, is discussed. Ct R2 has a different ligand structure than conventional class I R2 with a fourth Glu (like MMO) instead of three Glu and one Asp. Calculations indicate that, in the presence of Tyr, Glu at this position is less flexible than Asp, whereas with Phe both Glu and Asp are equally flexible. This may be a reason why conventional class I RNR has an Asp, while Ct R2, lacking the tyrosine, has a Glu.

Class I Ribonucleotide Reductases: Metallocofactor Assembly and Repair In Vitro and In Vivo

“…Thus, the ability of a Tyr or Trp radical in the PCET pathway to reoxidize a Fe III Fe III cluster to Fe IV Fe III seems unlikely (44, 133). A recent density functional theory study has come to the same conclusion (134). However, the possibility that the class Ic RNRs catalyze only a single turnover, with the cofactor regenerated by a specific repair pathway or de novo biosynthetic pathway for every dNDP produced (131), cannot be ruled out.…”

Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case study

“…The history of the discovery of the C. trachomatis class Ic RNR’s Mn IV Fe III cofactor has been recently reviewed 29,30,145,146 and will not be described in detail here. Important unresolved issues remain, however, including whether the Fe III Fe IV form is totally inactive 23 or can catalyze a single turnover 147,148 and the identity of the physiological cofactor. Because the in vivo metallation state of class Ic RNRs has not been established and because the class Ib RNRs are the only RNRs that can catalyze multiple turnovers using two different cofactors, we primarily restrict our remaining discussion to the class Ib RNR.…”

Assembly of nonheme Mn/Fe active sites in heterodinuclear metalloproteins

“…Calculations suggest that the radical equivalent Mn IV /Fe III redox state in R2c is an equally strong oxidant as the tyrosyl radical in E. coli R2a [119], so the redox potential of the Mn IV /Fe III state is likely commensurate with that of the active site cysteinyl radical in the R1 subunit. The heterodinuclear cofactor may thus represent a pure bioinorganic solution to produce a metal-centered radical-equivalent state allowing reversible radical transfer which the Fe IV /Fe III center would probably not allow as it would be too strong an oxidant.…”