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Title: Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli

Journal Article · · eLife
DOI:https://doi.org/10.7554/eLife.07141· OSTI ID:1236264
 [1];  [2];  [2];  [2];  [2]
  1. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Harvard Univ., Cambridge, MA (United States)
  2. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
+ Show Author Affiliations

Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site. In all characterized RNRs, the binding of effector dATP alters the active site to select for pyrimidines over purines, whereas effectors dGTP and TTP select for substrates ADP and GDP, respectively. Here, we have determined structures of Escherichia coli class Ia RNR with all four substrate/specificity effector-pairs bound (CDP/dATP, UDP/dATP, ADP/dGTP, GDP/TTP) that reveal the conformational rearrangements responsible for this remarkable allostery. These structures delineate how RNR ‘reads’ the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Inst. of Health; National Science Foundation (NSF); Howard Hughes Medical Inst.
Grant/Contract Number:
AC02-06CH11357; T32GM08334; P30-ES002109; 0645960
OSTI ID:
1236264
Journal Information:
eLife, Vol. 5, Issue 2015; ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.Copyright Statement
Country of Publication:
United States
Language:
ENGLISH
Citation Metrics:
Cited by: 48 works
Citation information provided by
Web of Science

References (44)

Rat liver thioredoxin and thioredoxin reductase: purification and characterization journal December 1982
Pre-Steady-State and Steady-State Kinetic Analysis of E. coli Class I Ribonucleotide Reductase journal September 2003
Highly mutagenic and severely imbalanced dNTP pools can escape detection by the S-phase checkpoint journal March 2010
PELDOR Spectroscopy with DOPA-β2 and NH 2 Y-α2s:  Distance Measurements between Residues Involved in the Radical Propagation Pathway of E. coli Ribonucleotide Reductase
  • Seyedsayamdost, Mohammad R.; Chan, Clement T. Y.; Mugnaini, Veronica
  • Journal of the American Chemical Society, Vol. 129, Issue 51 https://doi.org/10.1021/ja076459b
journal December 2007
[20] Use of rapid kinetics methods to study the assembly of the diferric-tyrosyl radical cofactor of E. coli ribonucleotide reductase book January 1995
Deoxycytidine Triphosphate Deaminase: Characterization of an Escherichia coli Mutant Deficient in the Enzyme journal January 1971
Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase journal October 2004
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination journal September 1998
A New Mechanism-based Radical Intermediate in a Mutant R1 Protein Affecting the Catalytically Essential Glu 441 in Escherichia coli Ribonucleotide Reductase journal December 1997
Towards automated crystallographic structure refinement with phenix.refine journal March 2012
Microscopic p K a Values of Escherichia coli Thioredoxin † journal December 1997
Kinetics of Radical Intermediate Formation and Deoxynucleotide Production in 3-Aminotyrosine-Substituted Escherichia coli Ribonucleotide Reductases journal June 2011
Conformational exchange in the potassium channel blocker ShK journal December 2019
X-Ray Diffraction data from E. coli class Ia ribonucleotide reductase dATP inhibited complex bound to UDP and dATP, source of 5CNT structure dataset January 2016
X-Ray Diffraction data from E. coli class Ia ribonucleotide reductase dATP inhibited complex bound to ADP and dGTP, source of 5CNU structure dataset January 2016
X-Ray Diffraction data from E. coli class Ia ribonucleotide reductase dATP inhibited complex bound to CDP and dATP, source of 5CNS structure dataset January 2016
The Cys292→Ala Substitution in Protein R1 of Class I Ribonucleotide Reductase from Escherichia Coli has a Global Effect on Nucleotide Binding at the Specificity-Determining Allosteric Site journal October 1996
dcd (dCTP deaminase) gene of Escherichia coli: mapping, cloning, sequencing, and identification as a locus of suppressors of lethal dut (dUTPase) mutations. journal September 1992
Methodology To Probe Subunit Interactions in Ribonucleotide Reductases † journal December 2008
Oligomerization Status Directs Overall Activity Regulation of the Escherichia coli Class Ia Ribonucleotide Reductase journal October 2008
Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding journal August 1997
Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation journal March 2006
Mechanisms of mutagenesis in vivo due to imbalanced dNTP pools journal October 2010
Tangled Up in Knots: Structures of Inactivated Forms of E. coli Class Ia Ribonucleotide Reductase journal August 2012
X-Ray Diffraction data from E. coli class Ia ribonucleotide reductase dATP inhibited complex bound to GDP and TTP, source of 5CNV structure dataset January 2016
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome journal December 2019
Mutant R1 Proteins from Escherichia coli Class Ia Ribonucleotide Reductase with Altered Responses to dATP Inhibition journal January 2004
Role of effector binding in allosteric control of ribonucleoside diphosphate reductase journal November 1969
Features and development of Coot journal March 2010
Thiyl Radicals in Ribonucleotide Reductases journal January 1996
Generation of a stable, aminotyrosyl radical-induced  2 2 complex of Escherichia coli class Ia ribonucleotide reductase journal February 2013
Cloning, overproduction, and purification of the B2 subunit of ribonucleoside-diphosphate reductase. journal February 1986
Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase journal December 2011
Inactivation of Ribonucleotide Reductase by ( E )-2‘-Fluoromethylene-2‘-deoxycytidine 5‘-Diphosphate:  A Paradigm for Nucleotide Mechanism-Based Inhibitors † journal January 1996
Characterization of Escherichia coli thioredoxins with altered active site residues journal April 1990
Products of the inactivation of ribonucleoside diphosphate reductase from Escherichia coli with 2'-azido-2'-deoxyuridine 5'-diphosphate journal June 1987
Role of Arginine 293 and Glutamine 288 in Communication between Catalytic and Allosteric Sites in Yeast Ribonucleotide Reductase journal June 2012
Subunit and small-molecule interaction of ribonucleotide reductases via surface plasmon resonance biosensor analyses journal June 2010
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997
Structure of ribonucleotide reductase protein R1 journal August 1994
Enzymatic Synthesis of Deoxyribonucleotides journal June 1966
Nature of the free radical in ribonucleotide reductase from Escherichia coli. journal January 1977
Thioredoxin Reductase journal March 1967
Binding of substrates to Escherichia coli ribonucleotide reductase. journal June 1976

Cited By (8)

Glutamate 52-β at the α/β subunit interface of Escherichia coli class Ia ribonucleotide reductase is essential for conformational gating of radical transfer journal April 2017
Potent competitive inhibition of human ribonucleotide reductase by a nonnucleoside small molecule journal July 2017
Convergent allostery in ribonucleotide reductase journal June 2019
Effects of T592 phosphomimetic mutations on tetramer stability and dNTPase activity of SAMHD1 can not explain the retroviral restriction defect journal August 2016
The Cell Killing Mechanisms of Hydroxyurea journal November 2016
The role of dNTP metabolites in control of the embryonic cell cycle journal September 2019
Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer journal August 2018
An endogenous dAMP ligand in Bacillus subtilis class Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP journal April 2018

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