Diversity in Overall Activity Regulation of Ribonucleotide Reductase

Jonna, Venkateswara Rao; Crona, Mikael; Rofougaran, Reza; Lundin, Daniel; Johansson, Samuel; Brännström, Kristoffer; Sjöberg, Britt‐Marie; Hofer, Anders

doi:10.1074/jbc.m115.649624

Cited by 46 publications

(88 citation statements)

References 37 publications

(21 reference statements)

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“…For example, in the class Ia RNR from E. coli , binding of the downstream product dTTP leads to preferred binding of the substrate GDP and disfavors the binding of a different substrate UDP, which is converted to dTTP later in its metabolic pathway (Figure 16). In many class Ia RNRs, the α subunit additionally contains at least one copy of an N-terminal “ATP cone” motif, which can house a second allosteric site, known as the activity site 174 (Figure 17A, orange domains). Binding of ATP to this site increases the rate of reduction, whereas its deoxy form (dATP) acts as an inhibitor at this site.…”

Section: Solution X-ray Scatteringmentioning

confidence: 99%

X-ray Scattering Studies of Protein Structural Dynamics

et al. 2017

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X-ray scattering is uniquely suited to the study of disordered systems and thus has the potential to provide insight into dynamic processes where diffraction methods fail. In particular, while X-ray crystallography has been a staple of structural biology for more than half a century and will continue to remain so, a major limitation of this technique has been the lack of dynamic information. Solution X-ray scattering has become an invaluable tool in structural and mechanistic studies of biological macromolecules where large conformational changes are involved. Such systems include allosteric enzymes that play key roles in directing metabolic fluxes of biochemical pathways, as well as large, assembly-line type enzymes that synthesize secondary metabolites with pharmaceutical applications. Furthermore, crystallography has the potential to provide information on protein dynamics via the diffuse scattering patterns that are overlaid with Bragg diffraction. Historically, these patterns have been very difficult to interpret, but recent advances in X-ray detection have led to a renewed interest in diffuse scattering analysis as a way to probe correlated motions. Here, we will review X-ray scattering theory and highlight recent advances in scattering-based investigations of protein solutions and crystals, with a particular focus on complex enzymes.

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Section: Solution X-ray Scatteringmentioning

confidence: 99%

X-ray Scattering Studies of Protein Structural Dynamics

et al. 2017

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“…As essential enzymes in central metabolism 1,2 , RNRs have evolved two complex forms of allostery [3][4][5] : specificity regulation, which is conserved in all RNRs, and activity regulation, which is canonically attributed only to RNRs with an evolutionarily mobile, regulatory domain known as the ATP-cone 6 . In this study, we describe the emergence of a new, convergent form of activity regulation in the class Ib RNRs, a major subset of aerobic RNRs that lack ATP-cones [7][8][9][10][11] . The evolution of class Ib RNRs is particularly relevant to medicine as they are the primary aerobic RNRs used by a number of bacterial pathogens such as Bacillus anthracis, Mycobacterium tuberculosis, Staphylococcus aureus, and Streptococcus pneumoniae 12 .…”

Section: Introductionmentioning

confidence: 99%

“…1d). This site is housed in an evolutionarily mobile, ~100-residue ATP-cone domain composed of a 4-helix bundle and a 3-stranded β-sheet cap, which is typically found at the Nterminus of the α subunit 6,11,20 (Fig. 1d,f).…”

Section: Introductionmentioning

confidence: 99%

“…Studies of class Ia RNRs have shown that ATP-cone domains preferentially interface with other RNR chains (α or β) upon binding of dATP to form ring-shaped oligomers that are proposed to inhibit activity by preventing long-range RT 5,[25][26][27][28] . Whereas most class Ia RNRs have at least one ATP-cone, class Ib RNRs are notable for sharing a characteristic truncated ATP-cone sequence at the N-terminus of α (NrdE) and lacking key A-site residues 7,11,29 (Fig 1e-f, orange). Consistent with this, class Ib RNRs have generally shown a lack of activity regulation [7][8][9][10] .…”

Section: Introductionmentioning

confidence: 99%

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Convergent Allostery in Ribonucleotide Reductase

Thomas

Brooks

Burnim

et al. 2018

Preprint

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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 new 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 novel, inhibited 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.Convergent Allostery in Ribonucleotide Reductase W. C. Thomas, et al.

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“…25,32,33 In the absence of evidence to the contrary, the simplest assumption is that this α 2 β 2 arrangement of the active complex is conserved in Ct RNR (Figure 1C), though determination of the oligomeric states and structures of active complexes in RNRs from various organisms remains an area of active research. 34–37 Despite intense scrutiny, the active α 2 β 2 complex has evaded characterization at atomic resolution. Such characterization has been limited by the fact that α and β associate rather weakly ( K d in the 0.1–1 μM range) and the α 2 β 2 complex is in equilibrium with other oligomeric forms.…”

Section: Introductionmentioning

confidence: 99%

Direct Measurement of the Radical Translocation Distance in the Class I Ribonucleotide Reductase from Chlamydia trachomatis

et al. 2015

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Ribonucleotide reductases (RNRs) catalyze conversion of ribonucleotides to deoxyribonucleotides in all organisms via a free-radical mechanism that is essentially conserved. In class I RNRs, the reaction is initiated and terminated by radical translocation (RT) between the α and β subunits. In the class Ic RNR from Chlamydia trachomatis (Ct RNR), the initiating event converts the active S = 1 Mn(IV)/Fe(III) cofactor to the S = 1/2 Mn(III)/Fe(III) "RT-product" form in the β subunit and generates a cysteinyl radical in the α active site. The radical can be trapped via the well-described decomposition reaction of the mechanism-based inactivator, 2'-azido-2'-deoxyuridine-5'-diphosphate, resulting in the generation of a long-lived, nitrogen-centered radical (N•) in α. In this work, we have determined the distance between the Mn(III)/Fe(III) cofactor in β and N• in α to be 43 ± 1 Å by using double electron-electron resonance experiments. This study provides the first structural data on the Ct RNR holoenzyme complex and the first direct experimental measurement of the inter-subunit RT distance in any class I RNR.

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Diversity in Overall Activity Regulation of Ribonucleotide Reductase

Cited by 46 publications

References 37 publications

X-ray Scattering Studies of Protein Structural Dynamics

X-ray Scattering Studies of Protein Structural Dynamics

Convergent Allostery in Ribonucleotide Reductase

Direct Measurement of the Radical Translocation Distance in the Class I Ribonucleotide Reductase from Chlamydia trachomatis

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