Structural Basis for Adenosylcobalamin Activation in AdoCbl-Dependent Ribonucleotide Reductases
Larsson, Kart-Magnus ; Logan, Derek LU
and Nordlund, Par
(2010)
In ACS Chemical Biology
5(10).
p.933-942
- 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 Thermo toga 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... (More)
- 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 Thermo toga 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 alpha-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. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/1726266
- author
- Larsson, Kart-Magnus
; Logan, Derek
LU
and Nordlund, Par
- organization
- publishing date
- 2010
- type
- Contribution to journal
- publication status
- published
- subject
- in
- ACS Chemical Biology
- volume
- 5
- issue
- 10
- pages
- 933 - 942
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- wos:000282924500004
- scopus:77958085972
- ISSN
- 1554-8937
- DOI
- 10.1021/cb1000845
- language
- English
- LU publication?
- yes
- id
- 5cea9260-8faa-4a32-8aff-2f97b4f52012 (old id 1726266)
- date added to LUP
- 2016-04-01 10:29:19
- date last changed
- 2025-04-04 14:48:30
@article{5cea9260-8faa-4a32-8aff-2f97b4f52012,
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 Thermo toga 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 alpha-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.}},
author = {{Larsson, Kart-Magnus and Logan, Derek and Nordlund, Par}},
issn = {{1554-8937}},
language = {{eng}},
number = {{10}},
pages = {{933--942}},
publisher = {{The American Chemical Society (ACS)}},
series = {{ACS Chemical Biology}},
title = {{Structural Basis for Adenosylcobalamin Activation in AdoCbl-Dependent Ribonucleotide Reductases}},
url = {{http://dx.doi.org/10.1021/cb1000845}},
doi = {{10.1021/cb1000845}},
volume = {{5}},
year = {{2010}},
}