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Structure paper

TitleConvergent allostery in ribonucleotide reductase.
Journal, issue, pagesNat Commun, Vol. 10, Issue 1, Page 2653, Year 2019
Publish dateJun 14, 2019
AuthorsWilliam C Thomas / F Phil Brooks / Audrey A Burnim / John-Paul Bacik / JoAnne Stubbe / Jason T Kaelber / James Z Chen / Nozomi Ando /
PubMed AbstractRibonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for ...Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.
External linksNat Commun / PubMed:31201319 / PubMed Central
MethodsEM (helical sym.) / X-ray diffraction
Resolution2.5 - 6.0 Å
Structure data

9272

6mw3

EMDB-9272, PDB-6mw3:
EM structure of Bacillus subtilis ribonucleotide reductase inhibited filament composed of NrdE alpha subunit and NrdF beta subunit with dATP
Method: EM (helical sym.) / Resolution: 4.65 Å

9293

6myx

EMDB-9293, PDB-6myx:
EM structure of Bacillus subtilis ribonucleotide reductase inhibited double-helical filament of NrdE alpha subunit with dATP
Method: EM (helical sym.) / Resolution: 6.0 Å

PDB-6mt9:
X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit with TTP, ATP, and ADP
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-6mv9:
X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit with TTP and ADP
Method: X-RAY DIFFRACTION / Resolution: 2.95 Å

PDB-6mve:
Reduced X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit with TTP, ATP, and ADP
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

Chemicals

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

Source
  • bacillus subtilis (bacteria)
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / allostery / nucleotide metabolism / dATP / ATP / filament / PROTEIN FIBRIL

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