The Crystal Structure of A Ternary Complex of Betaine Aldehyde Dehydrogenase from Pseudomonas aeruginosa Provides New Insight into the Reaction Mechanism and Shows A Novel Binding Mode of the 2′-Phosphate of NADP+ and A Novel Cation Binding Site

González‐Segura, Lilian; Rudino‐Pinera, E.; Muñoz‐Clares, Rosario A.; Horjales, E.

doi:10.1016/j.jmb.2008.10.082

Cited by 65 publications

(87 citation statements)

References 58 publications

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“…After the hydride transfer, the reduced nicotinamide ring must exit the catalytic site to allow for the accessibility of a water molecule, which hydrolyzes the acyl-sulfur bond releasing the product. In agreement with this mechanism, numerous crystal structures of ALDH revealed two common conformations of the coenzyme, depending on its oxidation state: the extended ("hydride transfer") conformation of NAD(P) ϩ , with the nicotinamide ring positioned close to Cys-302; and the contracted ("hydrolysis") conformation of NAD(P)H, with the nicotinamide ring found outside of the catalytic site or disordered (4,5,7,10,25,27,30). The mechanism by which ALDHs sense the oxidation state of the bound coenzyme and control its conformation is not fully understood.…”

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confidence: 76%

“…Catalytic Glutamate Is Critical for Mobility and Correct Positioning of Coenzyme-Several studies have suggested that the invariant catalytic glutamate of ALDHs (Glu-268 in class 1 and 2 enzymes) participates in both acylation and deacylation stages of the ALDH catalysis (5,7,23,25). Specifically, it has been proposed that in the first step it deprotonates the catalytic cysteine prior to nucleophilic attack on the substrate, whereas in the second step it activates a water molecule to facilitate the hydrolysis of the acyl-enzyme intermediate.…”

Section: Discussionmentioning

confidence: 99%

“…In the case of class 1 and 2 ALDHs, the likely candidate to abstract a proton from Cys-302 is Glu-268 (5,10,20,22). The glutamate then shuttles the proton to bulk water before participating in the deacylation step of the reaction (10,25). Crystal structures of wild type C t -FDH in complex with NADP ϩ gave further support of the cysteine deprotonation: the covalent bond between its sulfur atom and the nicotinamide ring, predicted based on quantum mechanical/molecular mechanical simulations in ALDH2 (41,42) and directly observed in our structure, is possible only upon the loss of a proton from the sulfhydryl group (10).…”

Section: Discussionmentioning

confidence: 99%

“…Of note, Arg-644 is located about 20 Å from the active center. Curiously, in a recent paper, Gonzáles-Segura and coauthors (25) suggested that this "crystallographic water" molecule bound at the C terminus of helix G could be a potassium atom. Located in the inter-subunit interface, this atom seems to be critical for maintaining the tetrameric state of Pseudomonas aeruginosa betaine ALDH (44).…”

Section: Discussionmentioning

confidence: 99%

“…The resulting thiolate ion is likely stabilized by the positively charged nic-otinamide ring of the coenzyme and/or adjacent main chain amide groups. It has also been suggested that, in tetrameric class 1 and 2 ALDHs, the proton abstracted by Glu-268 is shuttled to bulk water (10,25). In addition, Glu-268 is also the most likely residue activating a water molecule in the deacylation step of the reaction (5,7,10,23,26).…”

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Conserved Catalytic Residues of the ALDH1L1 Aldehyde Dehydrogenase Domain Control Binding and Discharging of the Coenzyme

Tsybovsky¹,

Krupenko

2011

Journal of Biological Chemistry

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The C-terminal domain (C t -FDH) of 10-formyltetrahydrofolate dehydrogenase (FDH, ALDH1L1) is an NADP ؉ -dependent oxidoreductase and a structural and functional homolog of aldehyde dehydrogenases. Here we report the crystal structures of several C t -FDH mutants in which two essential catalytic residues adjacent to the nicotinamide ring of bound NADP ؉ , Cys-707 and Glu-673, were replaced separately or simultaneously. The replacement of the glutamate with an alanine causes irreversible binding of the coenzyme without any noticeable conformational changes in the vicinity of the nicotinamide ring. Additional replacement of cysteine 707 with an alanine (E673A/ C707A double mutant) did not affect this irreversible binding indicating that the lack of the glutamate is solely responsible for the enhanced interaction between the enzyme and the coenzyme. The substitution of the cysteine with an alanine did not affect binding of NADP ؉ but resulted in the enzyme lacking the ability to differentiate between the oxidized and reduced coenzyme: unlike the wild-type C t -FDH/NADPH complex, in the C707A mutant the position of NADPH is identical to the position of NADP ؉ with the nicotinamide ring well ordered within the catalytic center. Thus, whereas the glutamate restricts the affinity for the coenzyme, the cysteine is the sensor of the coenzyme redox state. These conclusions were confirmed by coenzyme binding experiments. Our study further suggests that the binding of the coenzyme is additionally controlled by a longrange communication between the catalytic center and the coenzyme-binding domain and points toward an ␣-helix involved in the adenine moiety binding as a participant of this communication.Enzymes belonging to the family of aldehyde dehydrogenases (ALDH) 3 are involved in conversions of a broad variety of aliphatic and aromatic aldehydes to their respective carboxylic acids (1-3). These enzymes are either dimers or tetramers of identical subunits (1). Numerous crystal structures showed that subunits of different ALDHs have very similar fold with each composed of catalytic, nucleotide binding, and oligomerization domains (4 -10).Two members of the family, cytosolic ALDH1 and mitochondrial ALDH2, are essential components of the pathway metabolizing ethanol (2, 11). ALDH2 is also involved in mediating the vasodilator activity of nitroglycerine (12). Furthermore, activation of this enzyme correlates with reduced ischemic heart damage in rodent models (13). The polymorphism in the ALDH2 gene found in about 40% of the Asian population causes decreased tolerance to alcohol in heterozygous and homozygous individuals (14). This ALDH2 genetic variant, ALDH2 * 2, has a lysine instead of a glutamate at position 487 within the oligomerization domain of the tetrameric enzyme. This substitution induces conformational changes at the subunit interface, which are reflected by structural alterations within the catalytic center and the coenzyme binding site (5, 15, 16). The final outcome is a strong decrease in the affinity for NAD ...

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confidence: 76%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Conserved Catalytic Residues of the ALDH1L1 Aldehyde Dehydrogenase Domain Control Binding and Discharging of the Coenzyme

Tsybovsky¹,

Krupenko

2011

Journal of Biological Chemistry

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Oxidation of Alcohols, Aldehydes, and Acids

Hollmann

Bühler

2012

Enzyme Catalysis in Organic Synthesis

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Structural Insight into the Catalytic Mechanisms of an L‐Sorbosone Dehydrogenase

Li,

Deng,

Hou

et al. 2023

Advanced Science

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L‐Sorbosone dehydrogenase (SNDH) is a key enzyme involved in the biosynthesis of 2‐keto‐L‐gulonic acid , which is a direct precursor for the industrial scale production of vitamin C. Elucidating the structure and the catalytic mechanism is essential for improving SNDH performance. By solving the crystal structures of SNDH from Gluconobacter oxydans WSH‐004, a reversible disulfide bond between Cys295 and the catalytic Cys296 residues is discovered. It allowed SNDH to switch between oxidation and reduction states, resulting in opening or closing the substrate pocket. Moreover, the Cys296 is found to affect the NADP+ binding pose with SNDH. Combining the in vitro biochemical and site‐directed mutagenesis studies, the redox‐based dynamic regulation and the catalytic mechanisms of SNDH are proposed. Moreover, the mutants with enhanced activity are obtained by extending substrate channels. This study not only elucidates the physiological control mechanism of the dehydrogenase, but also provides a theoretical basis for engineering similar enzymes.

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The Crystal Structure of A Ternary Complex of Betaine Aldehyde Dehydrogenase from Pseudomonas aeruginosa Provides New Insight into the Reaction Mechanism and Shows A Novel Binding Mode of the 2′-Phosphate of NADP+ and A Novel Cation Binding Site

Cited by 65 publications

References 58 publications

Conserved Catalytic Residues of the ALDH1L1 Aldehyde Dehydrogenase Domain Control Binding and Discharging of the Coenzyme

Conserved Catalytic Residues of the ALDH1L1 Aldehyde Dehydrogenase Domain Control Binding and Discharging of the Coenzyme

Oxidation of Alcohols, Aldehydes, and Acids

Structural Insight into the Catalytic Mechanisms of an L‐Sorbosone Dehydrogenase

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