Ribonucleotide reductase crystal structure

Logan, D. T., Su, X. D., berg, A., Regnstr m, K., Hajdu, J., Eklund, H., and Nordlund, P., 1996, Crystal structure of reduced protein R2 of ribonucleotide reductase The structural basis for oxygen activation at a dinuclear iron site. Structure 4 1053nl064. 

A four-pulse DEER measurement of the distance between two tyrosyl radicals on the monomers that make up the R2 subunit of E. coli ribonucleotide reductase gave a point-dipole distance of 33.1 A, which is in good agreement with the X-ray crystal structure.84 Better agreement between the calculated and observed dipolar frequency could be obtained by summing contributions from distributed... 

Unfortunately, despite the great stability of the tyrosine radical of ribonucleotide reductase [69], the crystals available for diffraction contain the enzyme in its non-radical form [107]. However, the tyrosine residue (Tyr-122) known to convert to the radical is buried in the protein [99] and the position and structure of the tyrosine residue in the crystal is consistent with spectroscopic data for the radical form as with cytochrome c peroxidase, it appears unlikely that major conformational changes occur subsequent to radical formation. 

Figure 1. Structure of the R2 protein of E. coli ribonucleotide reductase in the met form. (Adapted from reference 7, which reports the 2.2 A crystal structure of the protein. Note that, in reference 7, Asp 84 is considered to be bidentate and chelating, but we prefer the mono dentate, hydrogen-bonded representation depicted above based on an analysis of the Fe-O distances.)...

Figure 2. Structure of a S211A mutant of the R2 protein of E. coli ribonucleotide reductase in the reduced form. (Adapted from reference 11 reporting the 2.2 A crystal structure.)...

Hsu, H., Dong, Y., Shu, L.,Young, J., V. G., and Que, J., L., 1999, Crystal structure of a synthetic high-valent complex with an Fc2(p-0)2 diamond core. Implications for the core structures of methane monooxygenase intermediate Q and ribonucleotide reductase intermediate X, J. Am. Chem. Soc. 121 5230n5237. 

Logan, D. T, deMarE, F., Persson, B. O., Slaby, A., Sj berg, B.-M., and Nordlund, P., 1998, Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants Structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins. Biochemistry 37 10798nl0807. 

D.T. Logan, J. Andersson, B.M. Sjoberg, and P. Nordlund. 1999. A glycyl radical site in the crystal structure of a class III ribonucleotide reductase Science 283 1499-1504. (PubMed)... 

From X-ray crystal structures the AT of the imidazole rings of the two histidine residues are coordinated to the Cu in plastocyanin (3, 4, 7), azurin (8), pseudoazurin (12), and CBP il3). However, in studies on Co(II)-substituted stellacyanin (71), it has been demonstrated that both histidines bind the metal via the N atom. Similar differences have been observed in the case of binuclear Fe proteins for example. Thus in ribonucleotide reductase the of histidine is coordinated, whereas in hemerythrin it is the N atom which is involved (85). In carbonic anhydrase the two coordinated imidazoles have and N atoms respectively bonded to the same Zn (85). The differences are most likely attributable to steric factors involving the polypeptide. 

Class I E. coli ribonucleotide reductase (RNR) exploits all the PCET variances of Fig. 17.3 in order to catalyze the reduction of nucleoside diphosphates to deoxynu-cleoside diphosphates. This reaction demands radical transport across two subunits and over a remarkable 35 A distance [187,188, 219]. The crystal structures of both R1 and R2 subunits have been solved independently [220-222] and a docking model has been proposed [220]. R2 harbors the diferric tyrosyl radical ( Y122) cofactor that initiates nucleotide reduction by generating a transient thiyl radical ( C439) in the enzyme active site located >35 A away in R1 [223]. Substrate conversion is initiated by a hydrogen atom abstraction (Type A PCET) at the 3 position of the substrate by C439 [192]. 

SiNTCHAK, M. D., ArJARA, G., Kellogg, B. A., Stubbe, J., Drennan, C. L. (2002) The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer, Nat. Struct. Biol. 9, 293-300. 

Although an X-ray crystal structure of MnRR has not been solved to date, a structure with Mn substituted into the iron ribonucleotide reductase has been reported (Fig. 6) (124). In this case, the two man-ganese(III) ions were bridged by two carboxylates from protein residues, but without the oxo bridge postulated for the active Fe1 form of the FeRR enzyme. This inactive enzyme with manganese was proposed as a model for the inactive Fe form of the iron enzyme and is... 

Lammers M, Follmann H (1983) The Ribonucleotide Reductases A unique Group of Metallo-enzymes Essential for Cell Proliferation. 54 27-91 Le Brun NE, Thomson AJ, Moore GR (1997) Metal Centres of Bacterioferritins or Non-Heam-Iron-Containing Cytochromes bs57. 88 103-138 Leciejewicz J, Alcock NW, Kemp TJ (1995) Carboxylato Complexes of the Uranyl Ion Effects of Ligand Size and Coordinate. Geometry Upon Molecular and Crystal Structure. 82 43-84... 

The ferroxidase center, important for rapid oxidation of Fe to Fe, was discovered relatively recently in the history of research into the metal sites in ferritins. Ferroxidase activity within H subunits appears to occur at a dinuclear site situated within a four-helix bundle and resembling the dinuclear centers found in ribonucleotide reductase, methane monooxygenase, fatty acid desaturases, and ruberythrin (Chapter 8.11). In bacterioferritins, for which protein crystal structures have been reported for ferritin from Escherichia col and Rhodobacter capsulatus the overall motif of a shell of 24 subunits with relative masses of about 18,500 Da is preserved but there are also 12 protoporphyrin IX heme groups present with unknown function which might have a role in connecting the dimer units and are buried within the shell between identical subunits related by twofold symmetry. In these bacterioferritins the subunits are all identical and contain both ftrroxidase and nucleation sites. 

The two chains of B1 are similar or identical in size but appear to differ somewhat in their N-terminal amino acid sequence. Thus, the overall composition of E. coli ribonucleotide reductase is of the type aa fi2- A schematic representation of the holoenzyme is reproduced in Fig. 2. Unfortunately the enzyme subunits could not as yet be obtained in crystals of sufficient size or stability for X-ray structure analysis. 

Ribonucleotide Reductase. The ribonucleotide reductases catalyze the reduction of ribonucleoside-diphosphates (or triphosphates) to the corresponding 2 -deoxyribonucleoside-diphosphates (or triphosphates), processes of preeminent importance for the biosynthesis of DNA (see Table 2, entry 4) (65,86). A variety of metal-containing cofactors have been discovered in the ribonucleotide reductases investigated to date (eg, a binuclear iron center in the mammalian and in the E. coli ribonucleoside diphosphate reductase) and the oxidation of two protein thiols to a disulfide unit is indicated as the direct source of the two reduction equivalents. The reductase from Lactobacillus leichmanii employs coenzyme B12 as cofactor in its (normal) base-on form and acts on purine- or pyrimidine-based ribonucleoside-triphosphates. Its crystal structure reveals not only the arrangement of the bound corrinoid cofactor, but also how the enzyme is... 

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