Substrate Locking Promotes Dimer-Dimer Docking of an Enzyme Antibiotic Target

Atkinson, Sarah C.; Dogovski, Con; Wood, Kathleen; Griffin, Michael D. W.; Gorman, Michael A.; Hor, Lilian; Reboul, Cyril; Buckle, Ashley M.; Wuttke, Joachim; Parker, Michael W.; Dobson, Renwick C. J.; Perugini, Matthew A.

doi:10.1016/j.str.2018.04.014

Cited by 6 publications

(3 citation statements)

References 102 publications

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“…We first examined the oligomeric structure of C LsoDHDPS, since DHDPS enzymes can form tetrameric (Atkinson et al, 2018 ; Dobson et al, 2005 ; Domigan et al, 2009 ) and/or dimeric structures (Atkinson et al, 2018 ; Burgess et al, 2008 ). The oligomeric state is known to be important for function because both the active site and the allosteric binding site comprise residues from the two monomers that form the tight‐interface (the yellow and green monomers in Figure 2b ) (Griffin et al, 2008 ; Pearce et al, 2011 ).…”

Section: Resultsmentioning

confidence: 99%

A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction

Gilkes,

Frampton,

Board

et al. 2024

Protein Science

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The effect of population bottlenecks and genome reduction on enzyme function is poorly understood. Candidatus Liberibacter solanacearum is a bacterium with a reduced genome that is transmitted vertically to the egg of an infected psyllid—a population bottleneck that imposes genetic drift and is predicted to affect protein structure and function. Here, we define the function of Ca. L. solanacearum dihydrodipicolinate synthase (CLsoDHDPS), which catalyzes the committed branchpoint reaction in diaminopimelate and lysine biosynthesis. We demonstrate that CLsoDHDPS is expressed in Ca. L. solanacearum and expression is increased ~2‐fold in the insect host compared to in planta. CLsoDHDPS has decreased thermal stability and increased aggregation propensity, implying mutations have destabilized the enzyme but are compensated for through elevated chaperone expression and a stabilized oligomeric state. CLsoDHDPS uses a ternary‐complex kinetic mechanism, which is to date unique among DHDPS enzymes, has unusually low catalytic ability, but an unusually high substrate affinity. Structural studies demonstrate that the active site is more open, and the structure of CLsoDHDPS with both pyruvate and the substrate analogue succinic‐semialdehyde reveals that the product is both structurally and energetically different and therefore evolution has in this case fashioned a new enzyme. Our study suggests the effects of genome reduction and genetic drift on the function of essential enzymes and provides insights on bacteria‐host co‐evolutionary associations. We propose that bacteria with endosymbiotic lifestyles present a rich vein of interesting enzymes useful for understanding enzyme function and/or informing protein engineering efforts.

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Section: Resultsmentioning

confidence: 99%

A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction

Gilkes,

Frampton,

Board

et al. 2024

Protein Science

View full text Add to dashboard Cite

show abstract

“…Such a mechanism of preserving active-site stability by oligomerization has been previously described, for example, dihydrodipicolinate synthase (DHDPS), which utilizes a tetrameric arrangement to stabilize the catalytic dimerization interface for optimal catalytic efficiency ( 41 ). Furthermore, formation of the DHDPS tetramer is promoted by substrate binding ( 42 ), thus, similarly to Pf A-M17, DHDPS demonstrates a complex interplay between substrate binding, oligomerization, and catalysis that is mediated by protein dynamics.…”

Section: Discussionmentioning

confidence: 99%

A metal ion–dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase

Webb¹,

Yang²,

Riley³

et al. 2022

Journal of Biological Chemistry

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“…We first examined the oligomeric structure of CLsoDHDPS, since DHDPS enzymes can form tetrameric (Dobson et al 2005;Domigan et al 2009;Atkinson et al 2018) and/or dimeric structures (Burgess et al 2008;Atkinson et al 2018). The oligomeric state is known to be important for function because both the active site and the allosteric binding site comprise residues from the two monomers that form the tight-interface (the yellow and green monomers in Figure 2B) (Griffin et al 2008;Pearce et al 2011).…”

Section: Crystal Structures Of Clsodhdps Demonstrate a Conserved Stru...mentioning

confidence: 99%

Genetic drift and genome reduction in the plant pathogenCandidatusLiberibacter solanacearum shapes a new enzyme in lysine biosynthesis

Gilkes

Frampton

Board

et al. 2023

Preprint

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The effect of population bottlenecks and genome reduction on enzyme function is poorly understood. 'Candidatus Liberibacter solanacearum' is a bacterium with a reduced genome that is transmitted vertically to the egg of an infected psyllid - a population bottleneck that imposes genetic drift and is predicted to affect protein structure and function. Here, we define the effects of genome reduction and genetic drift on the function of Ca. L. solanacearum dihydrodipicolinate synthase (CLsoDHDPS), which catalyses the committed branchpoint reaction in diaminopimelate and lysine biosynthesis. We demonstrate that CLsoDHDPS is expressed in Ca. L. solanacearum and expression is increased ~2-fold in the insect host compared to in planta. CLsoDHDPS has increased aggregation propensity, implying mutations have destabilised the enzyme but are compensated for through elevated chaperone expression and a stabilised oligomeric state. CLsoDHDPS uses a ternary-complex kinetic mechanism, which is unique among DHDPS enzymes, has unusually low catalytic ability, but an unusually high substrate affinity. Structural studies demonstrate that the active site is more open, and the structure of CLsoDHDPS with both pyruvate and the substrate analogue succinic-semialdehyde reveals that the product is both structurally and energetically different and therefore evolution has in this case fashioned a new enzyme. Our study reveals the effects of genome reduction and genetic drift on the function of essential enzymes and provides insights on bacteria-host co-evolutionary association. We suggest that bacteria with endosymbiotic lifestyles present a rich vein of interesting enzymes useful for understanding enzyme function and/or informing protein engineering efforts.

show abstract

Substrate Locking Promotes Dimer-Dimer Docking of an Enzyme Antibiotic Target

Cited by 6 publications

References 102 publications

A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction

A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction

A metal ion–dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase

Genetic drift and genome reduction in the plant pathogenCandidatusLiberibacter solanacearum shapes a new enzyme in lysine biosynthesis

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