Structural Mechanism of Allosteric Activity Regulation in a Ribonucleotide Reductase with Double ATP Cones

Structure, Journal Year: 2016, Volume and Issue: 24(6), P. 906 - 917

Published: April 30, 2016

Language: Английский

---

Convergent allostery in ribonucleotide reductase

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: June 14, 2019

Abstract Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides deoxyribonucleotides. Within RNR family, class Ib RNRs are notable for being largely restricted bacteria, including many pathogens, and lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report emergence distinct unexpected activity regulation in sole model organism Bacillus subtilis . Using hypothesis-driven structural approach combines strengths small-angle X-ray scattering (SAXS), crystallography, cryo-electron microscopy (cryo-EM), describe reversible interconversion six unique structures, flexible active tetramer two inhibited helical filaments. These structures reveal conformational gymnastics necessary molecular basis its control via convergent form allostery.

Language: Английский

---

Pseudomonas aeruginosa Exhibits Deficient Biofilm Formation in the Absence of Class II and III Ribonucleotide Reductases Due to Hindered Anaerobic Growth

Frontiers in Microbiology, Journal Year: 2016, Volume and Issue: 7

Published: May 9, 2016

Chronic lung infections by the ubiquitous and extremely adaptable opportunistic pathogen Pseudomonas aeruginosa correlate with formation of a biofilm, where bacteria grow in association an extracellular matrix display wide range changes gene expression metabolism. This leads to increased resistance physical stress antibiotic therapies, while enhancing cell-to-cell communication. Oxygen diffusion through complex biofilm structure generates oxygen concentration gradient, leading appearance anaerobic microenvironments. Ribonucleotide reductases (RNRs) are family highly sophisticated enzymes responsible for synthesis deoxyribonucleotides, they constitute only de novo pathway building blocks needed DNA repair. P. is one few encoding all three known RNR classes (Ia, II III). Class Ia RNRs dependent, class independent, III sensitive. A tight control activity essential growth therefore development. In this work we explored role different under aerobic initial conditions using static continuous-flow models. We demonstrated importance proper cell division development maturation. also determined that these transcriptionally induced during conditions. The molecular mechanism their regulation was studied, finding Anr/Dnr system induction. These data can be integrated previous knowledge about biofilms model structures understood as set layers contain cells profiles, bringing us step closer understanding pattern, chronic infections.

Language: Английский

---

A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: May 16, 2022

Abstract Ribonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, RNR-specific repressor, controls transcription RNR genes and, often, its own, most bacteria and some archaea. NrdR senses concentration nucleotides through ATP-cone, evolutionarily mobile domain also regulates enzymatic activity many RNRs, while a Zn-ribbon mediates binding to boxes upstream overlapping start site genes. Here, we combine biochemical cryo-EM studies from Streptomyces coelicolor show, at atomic resolution, how binds DNA. The suggested mechanism involves initial dodecamer loaded with two ATP molecules cannot bind When dATP concentrations increase, octamer forms one molecule each per monomer. A tetramer derived this then represses RNR. In — including well-known pathogens such as Mycobacterium tuberculosis simultaneously multiple RNRs hence synthesis, making it excellent target for novel antibiotics development.

Language: Английский

---

Bacterial transcriptional repressor NrdR – a flexible multifactorial nucleotide sensor

FEBS Journal, Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

NrdR is a bacterial transcriptional repressor consisting of zinc (Zn)‐ribbon domain followed by an ATP‐cone domain. Understanding its mechanism action could aid the design novel antibacterials. binds specifically to two “NrdR boxes” upstream ribonucleotide reductase operons, which Escherichia coli has three: nrdHIEF, nrdDG and nrdAB, in last we identified new box. We show that E. (EcoNrdR) similar binding strength all three sites when loaded with ATP plus deoxyadenosine triphosphate (dATP) or equivalent diphosphate combinations. No other combination adenine nucleotides promotes DNA. present crystal structures EcoNrdR–ATP–dATP EcoNrdR–ADP–dATP, are first high‐resolution NrdR. have also determined cryo‐electron microscopy DNA‐bound filaments EcoNrdR–ATP. Tetrameric forms EcoNrdR involve alternating interactions between pairs Zn‐ribbon domains ATP‐cones. The reveal considerable flexibility relative orientation ATP‐cones vs domains. structure shows significant conformational rearrangements Zn‐ribbons accompany DNA while retain same orientation. In contrast, ATP‐loaded sequester DNA‐binding residues such they unable bind Our results, previous structural biochemical study, point highly flexible that, correct nucleotides, adapt optimal promoter‐binding conformation.

Language: Английский

---