Structural insights into betaine aldehyde dehydrogenase (BADH2) from Oryza sativa explored by modeling and simulations

Scientific Reports
Apisara BaicharoenPrapasiri Pongprayoon

Abstract

Betaine aldehyde dehydrogenase 2 (BADH2) plays a key role in the accumulation of 2-acetyl-1-pyrroline (2AP), a fragrant compound in rice (Oryza sativa). BADH2 catalyses the oxidation of aminoaldehydes to carboxylic acids. An inactive BADH2 is known to promote fragrance in rice. The 3D structure and atomic level protein-ligand interactions are currently unknown. Here, the 3D dimeric structure of BADH2 was modeled using homology modeling. Furthermore, two 0.5 µs simulations were performed to explore the nature of BADH2 dimer structurally and dynamically. Each monomer comprises of 3 domains (substrate-binding, NAD+-binding, and oligomerization domains). The NAD+-binding domain is the most mobile. A scissor-like motion was observed between the monomers. Inside the binding pocket, N162 and E260 are tethered by strong hydrogen bonds to residues in close proximity. In contrast, the catalytic C294 is very mobile and interacts occasionally with N162. The flexibility of the nucleophilic C294 could facilitate the attack of free carbonyl on an aldehyde substrate. Key inter-subunit salt bridges contributing to dimerization were also identified. E487, D491, E492, K498, and K502 were found to form strong salt bridges with charged residues on ...Continue Reading

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Citations

Jun 20, 2019·Journal of Biomolecular Structure & Dynamics·Prapasiri PongprayoonSathaporn Jittapalapong
Jul 3, 2021·International Journal of Molecular Sciences·Vacha BhattAltafhusain Nadaf

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Software Mentioned

BLAST
ClustalW webserver
hbond
ClustalW
house
MODELLER
GROMACS

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