One Step Forward in Exploration of Class II Pyruvate Aldolases Nucleophile and Electrophile Substrate Specificity

Tagne, Rolande Ngahan; Laurent, Victor; Hélaine, Virgil; Petit, Jean-Louis; Traı̈kia, Mounir; Berardinis, Véronique de; Lemaire, Marielle; Guérard-Hélaine, Christine

doi:10.1002/cctc.202100932

“…The class II PDA typically contain divalent metal ions, ranging from Mg(II) to Co(II). They have recently been studied for their synthetic utility with a focus on expanding the range of donor molecules beyond pyruvate (de Berardinis et al 2017;Fang et al 2019;Gastaldi et al 2021;Laurent et al 2020;Marsden et al 2019). When studying Sphingomonas wittichii RW1 hydroketoacid aldoxy lase (SwHKA; recently the name of the organism was altered to Rhizorhabdus wittichii RW1), the active site was found to be located at the interface of two Fig.…”

Section: Class II Pyruvate-dependent Aldolasesmentioning

confidence: 99%

The metal cofactor: stationary or mobile?

Hagedoorn,

Pabst,

Hanefeld

2024

Appl Microbiol Biotechnol

1

0

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Metal cofactors are essential for catalysis and enable countless conversions in nature. Interestingly, the metal cofactor is not always static but mobile with movements of more than 4 Å. These movements of the metal can have different functions. In the case of the xylose isomerase and medium-chain dehydrogenases, it clearly serves a catalytic purpose. The metal cofactor moves during substrate activation and even during the catalytic turnover. On the other hand, in class II aldolases, the enzymes display resting states and active states depending on the movement of the catalytic metal cofactor. This movement is caused by substrate docking, causing the metal cofactor to take the position essential for catalysis. As these metal movements are found in structurally and mechanistically unrelated enzymes, it has to be expected that this metal movement is more common than currently perceived. Key points • Metal ions are essential cofactors that can move during catalysis. • In class II aldolases, the metal cofactors can reside in a resting state and an active state. • In MDR, the movement of the metal cofactor is essential for substrate docking. Graphical abstract

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“…[15] Its synthetic potential has been demonstrated for the conversion of various pyruvate analogues, including hydroxypyruvate, [14,15] fluoropyruvate [16] and 2oxobutyrate [17] and derivatives. [18][19][20] Based on these reports, we conducted a detailed structural characterization of SwHKA, which revealed two metal cofactor coordination sites of distinct properties. In contrast to allosteric regulation, the structural changes between the enzyme's active (M 2 + A ) and resting state (M 2 + R ) configurations are confined to the position of the metal cofactor.…”

Section: Introductionmentioning

confidence: 98%

“…Notably, Sw HKA is activated by trace amounts of inorganic phosphate ( K d,Pi =175 μM), which effect a rate enhancement of up to two orders in magnitude for the first step of the aldol reaction, the deprotonation of the pyruvate [15] . Its synthetic potential has been demonstrated for the conversion of various pyruvate analogues, including hydroxypyruvate, [14, 15] fluoropyruvate [16] and 2‐oxobutyrate [17] and derivatives [18–20] . Based on these reports, we conducted a detailed structural characterization of Sw HKA, which revealed two metal cofactor coordination sites of distinct properties.…”

Section: Introductionmentioning

confidence: 99%

Substrate Induced Movement of the Metal Cofactor between Active and Resting State

Marsden

¹

,

Wijma

²

,

Mohr

³

et al. 2022

Angewandte Chemie

0

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Regulation of enzyme activity is vital for living organisms. In metalloenzymes, far-reaching rearrangements of the protein scaffold are generally required to tune the metal cofactor's properties by allosteric regulation. Here structural analysis of hydroxyketoacid aldolase from Sphingomonas wittichii RW1 (SwHKA) revealed a dynamic movement of the metal cofactor between two coordination spheres without protein scaffold rearrangements. In its resting state configuration (M 2 + R ), the metal constitutes an integral part of the dimer interface within the overall hexameric assembly, but sterical constraints do not allow for substrate binding. Conversely, a second coordination sphere constitutes the catalytically active state (M 2 + A ) at 2.4 Å distance. Bidentate coordination of a ketoacid substrate to M 2 + A affords the overall lowest energy complex, which drives the transition from M 2 + R to M 2 + A . While not described earlier, this type of regulation may be widespread and largely overlooked due to low occupancy of some of its states in protein crystal structures.

show abstract

“…Notably, Sw HKA is activated by trace amounts of inorganic phosphate ( K d,Pi =175 μM), which effect a rate enhancement of up to two orders in magnitude for the first step of the aldol reaction, the deprotonation of the pyruvate [15] . Its synthetic potential has been demonstrated for the conversion of various pyruvate analogues, including hydroxypyruvate, [14, 15] fluoropyruvate [16] and 2‐oxobutyrate [17] and derivatives [18–20] . Based on these reports, we conducted a detailed structural characterization of Sw HKA, which revealed two metal cofactor coordination sites of distinct properties.…”

Section: Introductionmentioning

confidence: 99%

“… [15] Its synthetic potential has been demonstrated for the conversion of various pyruvate analogues, including hydroxypyruvate,[ 14 , 15 ] fluoropyruvate [16] and 2‐oxobutyrate [17] and derivatives. [ 18 , 19 , 20 ] Based on these reports, we conducted a detailed structural characterization of Sw HKA, which revealed two metal cofactor coordination sites of distinct properties. In contrast to allosteric regulation, the structural changes between the enzyme's active (M 2+ A ) and resting state (M 2+ R ) configurations are confined to the position of the metal cofactor.…”

Section: Introductionmentioning

confidence: 99%

Substrate Induced Movement of the Metal Cofactor between Active and Resting State

Marsden

¹

,

Wijma

²

,

Mohr

³

et al. 2022

Angew Chem Int Ed

3

0

View full text Add to dashboard Cite

Regulation of enzyme activity is vital for living organisms. In metalloenzymes, far-reaching rearrangements of the protein scaffold are generally required to tune the metal cofactor's properties by allosteric regulation. Here structural analysis of hydroxyketoacid aldolase from Sphingomonas wittichii RW1 (SwHKA) revealed a dynamic movement of the metal cofactor between two coordination spheres without protein scaffold rearrangements. In its resting state configuration (M 2 + R ), the metal constitutes an integral part of the dimer interface within the overall hexameric assembly, but sterical constraints do not allow for substrate binding. Conversely, a second coordination sphere constitutes the catalytically active state (M 2 + A ) at 2.4 Å distance. Bidentate coordination of a ketoacid substrate to M 2 + A affords the overall lowest energy complex, which drives the transition from M 2 + R to M 2 + A . While not described earlier, this type of regulation may be widespread and largely overlooked due to low occupancy of some of its states in protein crystal structures.

show abstract

One Step Forward in Exploration of Class II Pyruvate Aldolases Nucleophile and Electrophile Substrate Specificity

Abstract: This publication is part of a joint Special Collection with ChemBioChem on "BioTrans 2021". Please see our homepage for more articles in the collection. Scheme 1. Examples of 2-ethyl substituted 3-hydroxycarboxylic acids as chiral building blocks.

Cited by 5 publications

References 26 publications

The metal cofactor: stationary or mobile?

The metal cofactor: stationary or mobile?

Substrate Induced Movement of the Metal Cofactor between Active and Resting State

Substrate Induced Movement of the Metal Cofactor between Active and Resting State

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