Aldehyde Dehydrogenase Catalytic Mechanism

Hempel, John; Perozich, John; Chapman, Toby M.; Rose, John P.; Boesch, Josette S.; Liu, Zhijie; Lindahl, Ronald; Wang, Bi-Cheng

doi:10.1007/978-1-4615-4735-8_7

Cited by 49 publications

(49 citation statements)

References 13 publications

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“…This may indicate that once Cys-132 has been deprotonated by base attack from the bound water, the resulting hydronium ion is released and the thiolate side chain turns toward the bound cofactor in preparation for nucleophilic attack on the aldehyde intermediate. Such a mechanism has been postulated for CoA-independent aldehyde dehydrogenases (33).…”

Section: Resultsmentioning

confidence: 90%

Crystal structure of a bifunctional aldolase–dehydrogenase: Sequestering a reactive and volatile intermediate

Manjasetty

Powlowski

Vrielink

2003

Proc. Natl. Acad. Sci. U.S.A.

137

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The crystal structure of the bifunctional enzyme 4-hydroxy-2-ketovalerate aldolase (DmpG)͞acylating acetaldehyde dehydrogenase (DmpF), which is involved in the bacterial degradation of toxic aromatic compounds, has been determined by multiwavelength anomalous dispersion (MAD) techniques and refined to 1.7-Å resolution. Structures of the two polypeptides represent a previously unrecognized subclass of metal-dependent aldolases, and of a CoA-dependent dehydrogenase. The structure reveals a mixed state of NAD ؉ binding to the DmpF protomer. Domain movements associated with cofactor binding in the DmpF protomer may be correlated with channeling and activity at the DmpG protomer. In the presence of NAD ؉ a 29-Å-long sequestered tunnel links the two active sites. Two barriers are visible along the tunnel and suggest control points for the movement of the reactive and volatile acetaldehyde intermediate between the two active sites. E nzymatic channeling is a process by which intermediates are moved directly between active sites in a sequential reaction pathway without equilibrating with the bulk phase (1, 2). Channeling processes are particularly advantageous over the free diffusion of reaction products through the bulk solvent because they can protect chemically labile intermediates from breakdown, prevent loss of nonpolar intermediates by diffusion across cell membranes, or protect the cell from toxic intermediates. Crystallographic studies on a number of different enzyme systems involved in substrate channeling (3-11) have revealed important structural factors that mediate intersubunit or interdomain communication and facilitate the efficient transfer of intermediates between distant active sites.A bifunctional aldolase-dehydrogenase catalyzes the final two steps of the meta-cleavage pathway for catechol, an intermediate in many bacterial species in the degradation of phenols, toluates, naphthalene, biphenyls and other aromatic compounds (reviewed in ref. 12). Thus, 4-hydroxy-2-ketovalerate aldolase (DmpG; EC 4.1.3.-) and acetaldehyde dehydrogenase (acylating) (DmpF; EC 1.2.1.10) from a methylphenol-degrading pseudomonad convert 4-hydroxy-2-ketovalerate to pyruvate and acetyl-CoA by way of the intermediate acetaldehyde (Scheme 1).The two enzymes are tightly associated with each other (13,14). Whereas the aldolase appears to be inactive when expressed without the dehydrogenase, the dehydrogenase retains some activity when expressed in the absence of aldolase (14), suggesting that at least the dehydrogenase active site is distinct from that of the aldolase. Several lines of evidence are consistent with channeling of acetaldehyde between the active sites. For example, the conversion of 4-hydroxy-2-ketovalerate to acetyl-CoA occurs Ϸ20 times faster than that of acetaldehyde to acetyl-CoA, and the K m for acetaldehyde exceeds 50 mM, a physiologically irrelevant concentration (J.P., unpublished data). In addition, it has been shown that the aldolase activity is stimulated by the addition of the dehydrogenase cofactor to t...

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Section: Resultsmentioning

confidence: 90%

Crystal structure of a bifunctional aldolase–dehydrogenase: Sequestering a reactive and volatile intermediate

Manjasetty

Powlowski

Vrielink

2003

Proc. Natl. Acad. Sci. U.S.A.

137

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“…Depending on the specific ALDH, one or the other of these glutamate residues has been proposed to act as a general base that activates the cysteine nucleophile (20,38,43). Homologs to these glutamate residues can be found in BoxD at positions 255 and 399.…”

Section: Discussionmentioning

confidence: 99%

Aerobic Benzoyl-Coenzyme A (CoA) Catabolic Pathway in Azoarcus evansii : Conversion of Ring Cleavage Product by 3,4-Dehydroadipyl-CoA Semialdehyde Dehydrogenase

et al. 2006

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Benzoate, a strategic intermediate in aerobic aromatic metabolism, is metabolized in various bacteria via an unorthodox pathway. The intermediates of this pathway are coenzyme A (CoA) thioesters throughout, and ring cleavage is nonoxygenolytic. The fate of the ring cleavage product 3,4-dehydroadipyl-CoA semialdehyde was studied in the ␤-proteobacterium Azoarcus evansii. Cell extracts contained a benzoate-induced, NADP ؉ -specific aldehyde dehydrogenase, which oxidized this intermediate. A postulated putative long-chain aldehyde dehydrogenase gene, which might encode this new enzyme, is located on a cluster of genes encoding enzymes and a transport system required for aerobic benzoate oxidation. The gene was expressed in Escherichia coli, and the maltose-binding protein-tagged enzyme was purified and studied. It is a homodimer composed of 54 kDa (without tag) subunits and was confirmed to be the desired 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase. The reaction product was identified by nuclear magnetic resonance spectroscopy as the corresponding acid 3,4-dehydroadipyl-CoA. Hence, the intermediates of aerobic benzoyl-CoA catabolic pathway recognized so far are benzoyl-CoA; 2,3-dihydro-2,3-dihydroxybenzoyl-CoA; 3,4-dehydroadipyl-CoA semialdehyde plus formate; and 3,4-dehydroadipyl-CoA. The further metabolism is thought to lead to 3-oxoadipyl-CoA, the intermediate at which the conventional and the unorthodox pathways merge.

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“…3A) (Hempel et al, 1999): 1) activation of the catalytic Cys302 via a water-mediated proton abstraction by Glu268, 2) consequent nucleophilic attack on the electrophilic aldehyde by the thiolate group of Cys302, 3) formation of a tetrahedral thiohemiacetal intermediate (deacylation) with concomitant hydride transfer to the pyridine ring of NAD ϩ , 4) hydrolysis of the resulting thioester intermediate, and 5) dissociation of the reduced cofactor and subsequent regeneration of the enzyme by NAD ϩ binding. Glu268 functions as a general base required to activate the Cys302 through deprotonation, leading to the thiohemiacetal formation preceding the deacylation step (Wang and Weiner, 1995;Sheikh et al, 1997).…”

Section: B Structure and Catalysis Of Aldehyde Dehydrogenasementioning

confidence: 99%

Aldehyde Dehydrogenase Inhibitors: a Comprehensive Review of the Pharmacology, Mechanism of Action, Substrate Specificity, and Clinical Application

et al. 2012

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Aldehyde Dehydrogenase Catalytic Mechanism

Cited by 49 publications

References 13 publications

Crystal structure of a bifunctional aldolase–dehydrogenase: Sequestering a reactive and volatile intermediate

Crystal structure of a bifunctional aldolase–dehydrogenase: Sequestering a reactive and volatile intermediate

Aerobic Benzoyl-Coenzyme A (CoA) Catabolic Pathway in Azoarcus evansii : Conversion of Ring Cleavage Product by 3,4-Dehydroadipyl-CoA Semialdehyde Dehydrogenase

Aldehyde Dehydrogenase Inhibitors: a Comprehensive Review of the Pharmacology, Mechanism of Action, Substrate Specificity, and Clinical Application

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