Interdomain Conformational Changes Provide Allosteric Regulation en Route to Chorismate

Nazmi, Ali Reza; Lang, Eric J. M.; Bai, Yu; Allison, Timothy M.; Othman, Mohamad; Panjikar, Santosh; Arcus, Vickery L.; Parker, Emily J.

doi:10.1074/jbc.m116.741637

Cited by 23 publications

(91 citation statements)

References 51 publications

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“…Whereas type Ib contains a group of DAH7PS which has a discrete allosteric domain covalently linked to the catalytic barrel, such as the those from Thermotoga maritima 9 or Geobacillus sp ( Figure 1B). 10 The first fully characterized type II DAH7PS was from Mycobacterium tuberculosis (MtuDAH7PS, Figure 1C). 11,12 MtuDAH7PS contains both an N-terminal extension (three helices) and two other inserted helices to the core catalytic barrel, which constitute distinct allosteric binding sites specific to three different allosteric ligands (Trp, Phe and Tyr).…”

mentioning

confidence: 99%

A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis

Jiao

Fan

Blackmore

et al. 2020

Journal of Biological Chemistry

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Allostery exploits the conformational dynamics of enzymes by triggering a shift in population ensembles toward functionally distinct conformational or dynamic states. Allostery extensively regulates the activities of key enzymes within biosynthetic pathways to meet metabolic demand for their end products. Here, we have examined a critical enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS), at the gateway to aromatic amino acid biosynthesis in Mycobacterium tuberculosis, which shows extremely complex dynamic allostery: three distinct aromatic amino acids jointly communicate occupancy to the active site via subtle changes in dynamics, enabling exquisite fine-tuning of delivery of these essential metabolites. Furthermore, this allosteric mechanism is co-opted by pathway branchpoint enzyme chorismate mutase upon complex formation. In this study, using statistical coupling analysis, site-directed mutagenesis, isothermal calorimetry, small-angle X-ray scattering, and X-ray crystallography analyses, we have pinpointed a critical node within the complex dynamic communication network responsible for this sophisticated allosteric machinery. Through a facile Gly to Pro substitution, we have altered backbone dynamics, completely severing the allosteric signal yet remarkably, generating a nonallosteric enzyme that retains full catalytic activity. We also identified a second residue of prime importance to the inter-enzyme communication with chorismate mutase. Our results reveal that highly complex dynamic allostery is surprisingly vulnerable and provide further insights into the intimate link between catalysis and allostery.

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confidence: 99%

A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis

Jiao

Fan

Blackmore

et al. 2020

Journal of Biological Chemistry

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“…The dimer offers opportunities for the future study of allostery and chorismate biosynthesis in Burkholderia as previously investigated for Geobacillus sp. (Nazmi et al, 2016) and Mycobacterium tuberculosis (Munack et al, 2016…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of chorismate mutase from Burkholderia thailandensis

Asojo¹,

Dranow²,

Serbzhinskiy³

et al. 2018

Acta Cryst Sect F

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Burkholderia thailandensis is often used as a model for more virulent members of this genus of proteobacteria that are highly antibiotic-resistant and are potential agents of biological warfare that are infective by inhalation. As part of ongoing efforts to identify potential targets for the development of rational therapeutics, the structures of enzymes that are absent in humans, including that of chorismate mutase from B. thailandensis, have been determined by the Seattle Structural Genomics Center for Infectious Disease. The high-resolution structure of chorismate mutase from B. thailandensis was determined in the monoclinic space group P2 with three homodimers per asymmetric unit. The overall structure of each protomer has the prototypical AroQγ topology and shares conserved binding-cavity residues with other chorismate mutases, including those with which it has no appreciable sequence identity.

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“…In this species, DAHP synthase exists as a fusion protein with an N-terminal CM domain and is allosterically inhibited by prephenate, the product of CM. 107 SAXS studies revealed that a tighter association between the dimeric CM domains and the tetrameric DAHP synthase domains forms upon binding of prephenate, thus disrupting DAHP synthase function by occluding the active site. 107 Namely, Guinier analysis showed a subtle decrease in the radius of gyration R g from 36.5 ± 0.4 Å to 34.8 ± 0.6 Å in the presence of prephenate.…”

Section: Solution X-ray Scatteringmentioning

confidence: 99%

“…107 SAXS studies revealed that a tighter association between the dimeric CM domains and the tetrameric DAHP synthase domains forms upon binding of prephenate, thus disrupting DAHP synthase function by occluding the active site. 107 Namely, Guinier analysis showed a subtle decrease in the radius of gyration R g from 36.5 ± 0.4 Å to 34.8 ± 0.6 Å in the presence of prephenate. Evidence for compaction was also seen in the Kratky plots (Figure 5, blue to orange).…”

Section: Solution X-ray Scatteringmentioning

confidence: 99%

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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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Interdomain Conformational Changes Provide Allosteric Regulation en Route to Chorismate

Cited by 23 publications

References 51 publications

A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis

A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis

Crystal structure of chorismate mutase from Burkholderia thailandensis

X-ray Scattering Studies of Protein Structural Dynamics

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