Structural basis for adenosylcobalamin activation in AdoCbl-dependent ribonucleotide reductases.
Class II ribonucleotide reductases (RNR) catalyze the formation of an essential thiyl radical by homolytic cleavage of the Co-C bond in their adenosylcobalamin (AdoCbl) cofactor. Several mechanisms for the dramatic acceleration of Co-C bond cleavage in AdoCbl-dependent enzymes have been advanced, but no consensus yet exists. We present the structure of the class II RNR from Thermotoga maritima in three complexes: (i) with allosteric effector dTTP, substrate GDP, and AdoCbl; (ii) with dTTP and AdoCbl; (iii) with dTTP, GDP, and adenosine. Comparison of these structures gives the deepest structural insights so far into the mechanism of radical generation and transfer for AdoCbl-dependent RNR. AdoCbl binds to the active site pocket, shielding the substrate, transient 5'-deoxyadenosyl radical and nascent thiyl radical from solution. The e-propionamide side chain of AdoCbl forms hydrogen bonds directly to the α-phosphate group of the substrate. This interaction appears to cause a "locking-in" of the cofactor, and it is the first observation of a direct cofactor-substrate interaction in an AdoCbl-dependent enzyme. The structures support an ordered sequential reaction mechanism with release or relaxation of AdoCbl on each catalytic cycle. A conformational change of the AdoCbl adenosyl ribose is required to allow hydrogen transfer to the catalytic thiol group. Previously proposed mechanisms for radical transfer in B12-dependent enzymes cannot fully explain the transfer in class II RNR, suggesting that it may form a separate class that differs from the well-characterized eliminases and mutases.
Larsson
Karl-Magnus
KM
Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.
Logan
Derek T
DT
Nordlund
Pär
P
D000494:Allosteric Regulation; D003038:Cobamides / Q000378:metabolism*; D018360:Crystallography, X-Ray; D006153:Guanosine Diphosphate / Q000378:metabolism; D008958:Models, Molecular; D012264:Ribonucleotide Reductases / Q000737:chemistry* / Q000378:metabolism*; D020124:Thermotoga maritima / Q000737:chemistry / Q000201:enzymology*; D013942:Thymine Nucleotides / Q000378:metabolism
D003038:Cobamides; D013942:Thymine Nucleotides; D006153:Guanosine Diphosphate; D012264:Ribonucleotide Reductases; C000913:cobamamide; C024157:thymidine 5'-triphosphate