Convergent allostery in ribonucleotide reductase.

Allosteric Regulation / genetics Allosteric Site / genetics Bacillus subtilis / genetics Bacterial Proteins / chemistry Cryoelectron Microscopy Crystallography, X-Ray Evolution, Molecular Models, Molecular Protein Structure, Quaternary / genetics Ribonucleotide Reductases / chemistry Ribonucleotides / metabolism Scattering, Small Angle

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
14 06 2019
Historique:
received: 06 01 2019
accepted: 20 05 2019
entrez: 16 6 2019
pubmed: 16 6 2019
medline: 10 7 2019
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41467-019-10568-4 PMID: 31201319 PMC: PMC6572854
pubmed: 31201319
doi: 10.1038/s41467-019-10568-4
pii: 10.1038/s41467-019-10568-4
pmc: PMC6572854
doi:

Substances chimiques

Bacterial Proteins 0
Ribonucleotides 0
Ribonucleotide Reductases EC 1.17.4.-

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

2653

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM081393
Pays : United States
Organisme : NIGMS NIH HHS
ID : P30 GM124166
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM124847
Pays : United States
Organisme : U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
ID : GM081393
Pays : International
Organisme : NIGMS NIH HHS
ID : P41 GM103485
Pays : United States
Organisme : U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
ID : GM124847
Pays : International
Organisme : U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
ID : GM103485
Pays : International
Organisme : National Science Foundation (NSF)
ID : DMR-1332208
Pays : International

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Auteurs

William C Thomas (WC)

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.

F Phil Brooks (FP)

Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.

Audrey A Burnim (AA)

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
ORCID: 0000-0002-9962-1397

John-Paul Bacik (JP)

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.

JoAnne Stubbe (J)

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

Jason T Kaelber (JT)

Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
ORCID: 0000-0001-9426-1030

James Z Chen (JZ)

Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, 97239, USA.

Nozomi Ando (N)

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA. nozomi.ando@cornell.edu.
Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA. nozomi.ando@cornell.edu.

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Classifications MeSH

questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Régulation allostérique › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Sites de fixation › Site allostérique › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Bactéries › Bactéries à Gram positif › Bâtonnets à Gram positif › Bâtonnets sporulés à Gram positif › Bacillaceae › Bacillus › Bacillus subtilis › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines bactériennes › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Techniques d'investigation › Microscopie électronique › Cryomicroscopie électronique › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Techniques d'investigation › Techniques de chimie analytique › Cristallographie aux rayons X › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Phénomènes biologiques › Évolution biologique › Évolution moléculaire › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Techniques d'investigation › Modèles théoriques › Modèles moléculaires › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › Structure quaternaire des protéines › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Oxidoreductases › Ribonucleotide reductases › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Nucléotides › Ribonucléotides › Convergent allostery in ribonucleotide reductase.
questionsmedicales.fr › Phénomènes physiques › Diffusion de rayonnements › Diffusion aux petits angles › Convergent allostery in ribonucleotide reductase.