Aspartase/Fumarase Superfamily: A Common Catalytic Strategy Involving General Base-Catalyzed Formation of a Highly Stabilized <i>aci</i><b>-</b>Carboxylate Intermediate

Veetil, Vinod Puthan; Fibriansah, Guntur; Raj, Hans; Thunnissen, A.M.W.H.; Poelarends, Gerrit J.

doi:10.1021/bi300430j

Cited by 48 publications

(55 citation statements)

References 56 publications

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“…Hydration of an electron‐rich carbon double bond with the poor nucleophile water is a chemically challenging reaction and therefore nature normally prefers a conjugated electron‐poor double bond using the Michael reaction for alcohol formation using enzymes like aspartatases/fumarases, enoyl‐CoA hydratases and aconitases . Isomerization between ( S )‐linalool and geraniol is a basic chemical reaction, which was also found in a few other intramolecular hydroxyl transferases as i.e.…”

Section: Discussionmentioning

confidence: 99%

X‐ray structure of linalool dehydratase/isomerase from Castellaniella defragrans reveals enzymatic alkene synthesis

2016

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Edited by Stuart FergusonLinalool dehydratase/isomerase (Ldi), an enzyme of terpene degradation in Castellaniella defragrans, isomerizes the primary monoterpene alcohol geraniol into the tertiary alcohol (S)-linalool and dehydrates (S)-linalool to the alkene b-myrcene. Here we report on the crystal structures of Ldi with and without terpene substrates, revealing a cofactor-free homopentameric enzyme. The substrates were embedded inside a hydrophobic channel between two monomers of the (a,a) 6 barrel fold class and flanked by three clusters of polar residues involved in acid-base catalysis. The detailed view into the active site will guide future biotechnological applications of Ldi, in particular, for industrial butadiene and isoprene production from renewable sources.

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Section: Discussionmentioning

confidence: 99%

X‐ray structure of linalool dehydratase/isomerase from Castellaniella defragrans reveals enzymatic alkene synthesis

2016

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“…Three conserved regions (C1, C2, and C3), separated from each other in the monomer, gather from three different subunits to form one active site. Part of region C3 is a flexible loop (the ‘SS loop’) of the active site and contains the signature sequence GSSXXPXKXN that defines the aspartase/fumarase superfamily .…”

Section: Introductionmentioning

confidence: 99%

The complex allosteric and redox regulation of the fumarate hydratase and malate dehydratase reactions of Arabidopsis thaliana Fumarase 1 and 2 gives clues for understanding the massive accumulation of fumarate

et al. 2018

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Arabidopsis thaliana possesses two fumarase genes (FUM), AtFUM1 (At2g47510) encoding for the mitochondrial Krebs cycle-associated enzyme and AtFUM2 (At5g50950) for the cytosolic isoform required for fumarate massive accumulation. Here, the comprehensive biochemical studies of AtFUM1 and AtFUM2 shows that they are active enzymes with similar kinetic parameters but differential regulation. For both enzymes, fumarate hydratase (FH) activity is favored over the malate dehydratase (MD) activity; however, MD is the most regulated activity with several allosteric activators. Oxalacetate, glutamine, and/or asparagine are modulators causing the MD reaction to become preferred over the FH reaction. Activity profiles as a function of pH suggest a suboptimal FUM activity in Arabidopsis cells; moreover, the direction of the FUM reaction is sensitive to pH changes. Under mild oxidation conditions, AtFUMs form high mass molecular aggregates, which present both FUM activities decreased to a different extent. The biochemical properties of oxidized AtFUMs (oxAtFUMs) were completely reversed by NADPH-supplied Arabidopsis leaf extracts, suggesting that the AtFUMs redox regulation can be accomplished in vivo. Mass spectrometry analyses indicate the presence of an active site-associated intermolecular disulfide bridge in oxAtFUMs. Finally, a phylogenetic approach points out that other plant species may also possess cytosolic FUM2 enzymes mainly encoded by paralogous genes, indicating that the evolutionary history of this trait has been drawn through a process of parallel evolution. Overall, according to our results, a multilevel regulatory pattern of FUM activities emerges, supporting the role of this enzyme as a carbon flow monitoring point through the organic acid metabolism in plants.

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“…This superfamily also includes argininosuccinate lyase, δ2‐crystallin, class II fumarase, l ‐aspartase and 3‐carboxy‐ cis,cis ‐muconate lactonizing enzyme (CMLE). The sequence identity across the members of the superfamily is ~ 10–20% , yet they are uniquely characterized by a common fold and their ability to catalyze β‐elimination reactions of succinyl containing substrates leading to the formation of fumarate, except in the CMLE catalyzed reaction, which results in the formation of lactone .…”

Section: Resultsmentioning

confidence: 99%

Structural and kinetic studies on adenylosuccinate lyase from Mycobacterium smegmatis and Mycobacterium tuberculosis provide new insights on the catalytic residues of the enzyme

et al. 2014

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Adenylosuccinate lyase (ASL), an enzyme involved in purine biosynthesis, has been recognized as a drug target against microbial infections. In the present study, ASL from Mycobacterium smegmatis (MsASL) and Mycobacterium tuberculosis (MtbASL) were cloned, purified and crystallized. The X-ray crystal structure of MsASL was determined at a resolution of 2.16A. It is the first report of an apo-ASL structure with a partially ordered active site C3 loop. Diffracting crystals of MtbASL could not be obtained and a model for its structure was derived using MsASL as a template. These structures suggest that His149 and either Lys285 or Ser279 of MsASL are the residues most likely to function as the catalytic acid and base, respectively. Most of the active site residues were found to be conserved, with the exception of Ser148 and Gly319 of MsASL. Ser148 is structurally equivalent to a threonine in most other ASLs. Gly319 is replaced by an arginine residue in most ASLs. The two enzymes were catalytically much less active compared to ASLs from other organisms. Arg319Gly substitution and reduced flexibility of the C3 loop might account for the low catalytic activity of mycobacterial ASLs. The low activity is consistent with the slow growth rate of Mycobacteria and their high GC containing genomes, as well as their dependence on other salvage pathways for the supply of purine nucleotides. Structured digital abstract• purB and purB bind by x-ray crystallography (View interaction)

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Aspartase/Fumarase Superfamily: A Common Catalytic Strategy Involving General Base-Catalyzed Formation of a Highly Stabilized aci-Carboxylate Intermediate

Cited by 48 publications

References 56 publications

X‐ray structure of linalool dehydratase/isomerase from Castellaniella defragrans reveals enzymatic alkene synthesis

X‐ray structure of linalool dehydratase/isomerase from Castellaniella defragrans reveals enzymatic alkene synthesis

The complex allosteric and redox regulation of the fumarate hydratase and malate dehydratase reactions of Arabidopsis thaliana Fumarase 1 and 2 gives clues for understanding the massive accumulation of fumarate

Structural and kinetic studies on adenylosuccinate lyase from Mycobacterium smegmatis and Mycobacterium tuberculosis provide new insights on the catalytic residues of the enzyme

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