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Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense

View Article: PubMed Central - PubMed

ABSTRACT

3-Hydroxypropionic acid (3-HP) is an important platform chemical to be converted to acrylic acid and acrylamide. Aldehyde dehydrogenase (ALDH), an enzyme that catalyzes the reaction of 3-hydroxypropionaldehyde (3-HPA) to 3-HP, determines 3-HP production rate during the conversion of glycerol to 3-HP. To elucidate molecular mechanism of 3-HP production, we determined the first crystal structure of a 3-HP producing ALDH, α-ketoglutarate-semialdehyde dehydrogenase from Azospirillum basilensis (AbKGSADH), in its apo-form and in complex with NAD+. Although showing an overall structure similar to other ALDHs, the AbKGSADH enzyme had an optimal substrate binding site for accepting 3-HPA as a substrate. Molecular docking simulation of 3-HPA into the AbKGSADH structure revealed that the residues Asn159, Gln160 and Arg163 stabilize the aldehyde- and the hydroxyl-groups of 3-HPA through hydrogen bonds, and several hydrophobic residues, such as Phe156, Val286, Ile288, and Phe450, provide the optimal size and shape for 3-HPA binding. We also compared AbKGSADH with other reported 3-HP producing ALDHs for the crucial amino acid residues for enzyme catalysis and substrate binding, which provides structural implications on how these enzymes utilize 3-HPA as a substrate.

No MeSH data available.


Overall structure of AbKGSADH.(a) The monomeric structure of AbKGSADH. The monomeric structure of AbKGSADH is presented as a cartoon diagram. N-terminal domain (NTD), C-terminal domain (CTD), and oligomerization domain (OGD) are distinguished with light-blue, orange, and magenta colors, respectively, and labeled. The bound NAD+ from the crystal data and 3-HPA derived from molecular docking simulation are shown as sphere models with yellow and green colors, respectively. The left and right figures are rotated 90 degree vertically from the figure in the middle. (b) Tetrameric structure of AbKGSADH. The tetrameric structure of AbKGSADH is presented as a cartoon diagram. Mol I is presented with colors of light-blue, orange, and magenta for NTD, CTD, and OGD, respectively, and Mol II is presented with green color. The other two molecules are shown with grey colors. The bound NAD+ is presented as stick models with yellow color. The right figure is rotated by 90 degree vertically from the left figure.
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f2: Overall structure of AbKGSADH.(a) The monomeric structure of AbKGSADH. The monomeric structure of AbKGSADH is presented as a cartoon diagram. N-terminal domain (NTD), C-terminal domain (CTD), and oligomerization domain (OGD) are distinguished with light-blue, orange, and magenta colors, respectively, and labeled. The bound NAD+ from the crystal data and 3-HPA derived from molecular docking simulation are shown as sphere models with yellow and green colors, respectively. The left and right figures are rotated 90 degree vertically from the figure in the middle. (b) Tetrameric structure of AbKGSADH. The tetrameric structure of AbKGSADH is presented as a cartoon diagram. Mol I is presented with colors of light-blue, orange, and magenta for NTD, CTD, and OGD, respectively, and Mol II is presented with green color. The other two molecules are shown with grey colors. The bound NAD+ is presented as stick models with yellow color. The right figure is rotated by 90 degree vertically from the left figure.

Mentions: To elucidate the molecular mechanism of 3-HP producing ALDHs, we determined the crystal structure of AbKGSADH at a 2.25 Å resolution. The refined structure was in good agreement with the X-ray crystallographic statistics for bond angles, bond lengths, and other geometric parameters (Table 1). The overall structure of AbKGSADH shows a conventional conformation for the ALDH fold. The monomeric structure of AbKGSADH consists of three domains: two core domains and one oligomerization domain (OGD) (Fig. 2a). The core domains consist of the N-terminal domain (NTD) (Met1-Arg123 and Val145-Leu253) and the C-terminal domain (CTD) (Gly254-Pro469). The NTD is composed of seven α-helices (α1–α7) and nine β-strands (β1–β4 and β7–β11), and forms the NAD(P)-binding Rossmann fold, where seven β-strands (β1–β2 and β7–β11) form a large β-sheet packed in the middle of the domain and other two β-strands (β3–β4) are located on the surface of the domain. The three α-helices (α1, α6 and α7) and the four α-helices (α2–α5) occupy both sides of the central β-sheet (Fig. 2a). The CTD consists of seven α-helices (α8–α14) and seven β-strands (β12–β18). Seven β-strands are also packed as a large β-sheet in the middle of the domain. Six α-helices surround the central β-sheet and one α-helix (α14) is located between the NTD and the OGD. The OGD (Val124-Pro144 and Tyr470-Val481) has two long β-strands (β6 and β19) and one short β-strand (β5), which are packed in a line and protrude from the NTD (Fig. 2a).


Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense
Overall structure of AbKGSADH.(a) The monomeric structure of AbKGSADH. The monomeric structure of AbKGSADH is presented as a cartoon diagram. N-terminal domain (NTD), C-terminal domain (CTD), and oligomerization domain (OGD) are distinguished with light-blue, orange, and magenta colors, respectively, and labeled. The bound NAD+ from the crystal data and 3-HPA derived from molecular docking simulation are shown as sphere models with yellow and green colors, respectively. The left and right figures are rotated 90 degree vertically from the figure in the middle. (b) Tetrameric structure of AbKGSADH. The tetrameric structure of AbKGSADH is presented as a cartoon diagram. Mol I is presented with colors of light-blue, orange, and magenta for NTD, CTD, and OGD, respectively, and Mol II is presented with green color. The other two molecules are shown with grey colors. The bound NAD+ is presented as stick models with yellow color. The right figure is rotated by 90 degree vertically from the left figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5385487&req=5

f2: Overall structure of AbKGSADH.(a) The monomeric structure of AbKGSADH. The monomeric structure of AbKGSADH is presented as a cartoon diagram. N-terminal domain (NTD), C-terminal domain (CTD), and oligomerization domain (OGD) are distinguished with light-blue, orange, and magenta colors, respectively, and labeled. The bound NAD+ from the crystal data and 3-HPA derived from molecular docking simulation are shown as sphere models with yellow and green colors, respectively. The left and right figures are rotated 90 degree vertically from the figure in the middle. (b) Tetrameric structure of AbKGSADH. The tetrameric structure of AbKGSADH is presented as a cartoon diagram. Mol I is presented with colors of light-blue, orange, and magenta for NTD, CTD, and OGD, respectively, and Mol II is presented with green color. The other two molecules are shown with grey colors. The bound NAD+ is presented as stick models with yellow color. The right figure is rotated by 90 degree vertically from the left figure.
Mentions: To elucidate the molecular mechanism of 3-HP producing ALDHs, we determined the crystal structure of AbKGSADH at a 2.25 Å resolution. The refined structure was in good agreement with the X-ray crystallographic statistics for bond angles, bond lengths, and other geometric parameters (Table 1). The overall structure of AbKGSADH shows a conventional conformation for the ALDH fold. The monomeric structure of AbKGSADH consists of three domains: two core domains and one oligomerization domain (OGD) (Fig. 2a). The core domains consist of the N-terminal domain (NTD) (Met1-Arg123 and Val145-Leu253) and the C-terminal domain (CTD) (Gly254-Pro469). The NTD is composed of seven α-helices (α1–α7) and nine β-strands (β1–β4 and β7–β11), and forms the NAD(P)-binding Rossmann fold, where seven β-strands (β1–β2 and β7–β11) form a large β-sheet packed in the middle of the domain and other two β-strands (β3–β4) are located on the surface of the domain. The three α-helices (α1, α6 and α7) and the four α-helices (α2–α5) occupy both sides of the central β-sheet (Fig. 2a). The CTD consists of seven α-helices (α8–α14) and seven β-strands (β12–β18). Seven β-strands are also packed as a large β-sheet in the middle of the domain. Six α-helices surround the central β-sheet and one α-helix (α14) is located between the NTD and the OGD. The OGD (Val124-Pro144 and Tyr470-Val481) has two long β-strands (β6 and β19) and one short β-strand (β5), which are packed in a line and protrude from the NTD (Fig. 2a).

View Article: PubMed Central - PubMed

ABSTRACT

3-Hydroxypropionic acid (3-HP) is an important platform chemical to be converted to acrylic acid and acrylamide. Aldehyde dehydrogenase (ALDH), an enzyme that catalyzes the reaction of 3-hydroxypropionaldehyde (3-HPA) to 3-HP, determines 3-HP production rate during the conversion of glycerol to 3-HP. To elucidate molecular mechanism of 3-HP production, we determined the first crystal structure of a 3-HP producing ALDH, α-ketoglutarate-semialdehyde dehydrogenase from Azospirillum basilensis (AbKGSADH), in its apo-form and in complex with NAD+. Although showing an overall structure similar to other ALDHs, the AbKGSADH enzyme had an optimal substrate binding site for accepting 3-HPA as a substrate. Molecular docking simulation of 3-HPA into the AbKGSADH structure revealed that the residues Asn159, Gln160 and Arg163 stabilize the aldehyde- and the hydroxyl-groups of 3-HPA through hydrogen bonds, and several hydrophobic residues, such as Phe156, Val286, Ile288, and Phe450, provide the optimal size and shape for 3-HPA binding. We also compared AbKGSADH with other reported 3-HP producing ALDHs for the crucial amino acid residues for enzyme catalysis and substrate binding, which provides structural implications on how these enzymes utilize 3-HPA as a substrate.

No MeSH data available.