Structure and function of the radical enzyme ribonucleotide reductase

Abstract

Ribonucleotide reductases (RNRs) catalyze all new production in nature of deoxyribonucleotides for DNA synthesis by reducing the corresponding ribonucleotides. The reaction involves the action of a radical that is produced differently for different classes of the enzyme. Class I enzymes, which are present in eukaryotes and microorganisms, use an iron center to produce a stable tyrosyl radical that is stored in one of the subunits of the enzyme. The other classes are only present in microorganisms. Class II enzymes use cobalamin for radical generation and class III enzymes, which are found only in anaerobic organisms, use a glycyl radical. The reductase activity is in all three classes contained in enzyme subunits that have similar structures containing active site cysteines. The initiation of the reaction by removal of the 3'-hydrogen of the ribose by a transient cysteinyl radical is a common feature of the different classes of RNR. This cysteine is in all RNRs located on the tip of a finger loop inserted into the center of a special barrel structure. A wealth of structural and functional information on the class I and class III enzymes can now give detailed views on how these enzymes perform their task. The class I enzymes demonstrate a sophisticated pattern as to how the free radical is used in the reaction, in that it is only delivered to the active site at exactly the right moment. RNRs are also allosterically regulated, for which the structural molecular background is now starting to be revealed.

Biomimetic Modeling of the Nitrogen-centered Radical Postulated to occur during the Inhibition of Ribonucleotide Reductases by 2'-Azido-2'-deoxynucleotides.

“…Their cofactors contain a tyrosyl radical and a diferric iron center, which generate a thiyl radical C439 in the R1 subunit. 1,[10][11][12] The prototype of Class II RNRs was isolated from Lactobacillus leichmannii.…”

“…Adenosylcobalamin (AdoCbl), or coenzyme B 12 , acts as a cofactor for this monomeric enzyme. It has been suggested that AdoCbl abstracts the hydrogen atom from the cysteine residue (cys408) in the R1 subunit to form a thiyl radical, generating cob(II)alamin and, supposedly, an 5'-deoxyadenosyl radical.…”

“…It has been suggested that AdoCbl abstracts the hydrogen atom from the cysteine residue (cys408) in the R1 subunit to form a thiyl radical, generating cob(II)alamin and, supposedly, an 5'-deoxyadenosyl radical. 1,[10][11][12] The RNR that was isolated from the facultative anaerobic E. coli is the prototype of Class III RNRs. The prototypical Class III RNR has a quaternary structure containing a glycyl radical as the cofactor, which is formed from S-adenosylmethionine and an ironsulfur cluster.…”

“…Like other classes of RNRs, the glycyl radical also generates a thiyl radical in the R1 subunit. 1,[10][11][12] Class IV RNRs were isolated from Brevibacterium ammoniagenes, which in comparison to other classes of RNRs, have not been studied extensively. However, they also have the cofactor that generates a thiyl radical.…”

“…It is believed that the cofactor is composed of a dinuclear Mn 3+ cluster similar to the diferric cluster of the class I RNR. 1,[10][11][12] Class I RNRs, which was isolated from E. coli grown under aerobic conditions, are composed of two homodimeric subunits, R1 and R2 ( Figure 2). The structure of the R1 protein contains five cysteine residues, a glutamic acid residue, an aspargine residue, and allosteric-effector binding sites that execute important functions in the mechanism of ribonucleotide reduction.…”