3O0O

Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP, GDP and Adenosylcobalamin

Summary for 3O0O

• Entry DOI: 10.2210/pdb3o0o/pdb
• Related: 1XJE 1XJF 1XJG 1XJJ 1XJM 1XJN 3O0N 3O0Q
• Descriptor: Ribonucleoside-diphosphate reductase, THYMIDINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (7 entities in total)
• Functional Keywords: oxidoreductase, 10 alpha/beta barrel, adenosylcobalamin dependent, ribonucleotide reductase, reduction ribonucleotide 2'-oh position, effector, dttp, substrate, gdp, coenzyme b12
• Biological source: Thermotoga maritima
• Total number of polymer chains: 2
• Total formula weight: 151811.01

Authors

Larsson, K.-M.,Logan, D.T.,Nordlund, P. (deposition date: 2010-07-19, release date: 2010-07-28, Last modification date: 2023-09-06)

Primary citation

Larsson, K.M.,Logan, D.T.,Nordlund, P.
Structural Basis for Adenosylcobalamin Activation in AdoCbl-Dependent Ribonucleotide Reductases.
Acs Chem.Biol., 5:933-942, 2010

PubMed Abstract: 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.

PubMed: 20672854
DOI: 10.1021/cb1000845

Experimental method

X-RAY DIFFRACTION (1.9 Å)