Literature summary for 1.1.1.331 extracted from

Youn, B.; Moinuddin, S.G.; Davin, L.B.; Lewis, N.G.; Kang, C.
Crystal structures of apo-form and binary/ternary complexes of Podophyllum secoisolariciresinol dehydrogenase, an enzyme involved in formation of health-protecting and plant defense lignans (2005), J. Biol. Chem., 280, 12917-12926.

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Crystallization (Commentary)

Crystallization (Comment)	Organism
crystal structures of the apo-form and binary/ternary complexes at 1.6, 2.8, and 2.0 A resolution, respectively. The enzyme is a homotetramer, consisting of an alpha/beta single domain monomer containing seven parallel beta-strands flanked by eight alpha-helices on both sides. Its overall monomeric structure shows a conserved Asp47 residue forming a hydrogen bond with both hydroxyl groups of the adenine ribose of NAD(H), and thus specificity toward NAD(H) instead of NADP(H). The highly conserved catalytic triad Ser153, Tyr167, and Lys171 is adjacent to both NAD(H) and substrate molecules, where Tyr167 functions as a general base	Podophyllum peltatum

Crystallization (Comment)

Organism

crystal structures of the apo-form and binary/ternary complexes at 1.6, 2.8, and 2.0 A resolution, respectively. The enzyme is a homotetramer, consisting of an alpha/beta single domain monomer containing seven parallel beta-strands flanked by eight alpha-helices on both sides. Its overall monomeric structure shows a conserved Asp47 residue forming a hydrogen bond with both hydroxyl groups of the adenine ribose of NAD(H), and thus specificity toward NAD(H) instead of NADP(H). The highly conserved catalytic triad Ser153, Tyr167, and Lys171 is adjacent to both NAD(H) and substrate molecules, where Tyr167 functions as a general base

Podophyllum peltatum

Organism

Organism	UniProt	Comment	Textmining
Podophyllum peltatum	Q94KL8	fragment	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
(-)-secoisolariciresinol + 2 NAD+	nicotinamide and the substrate are in the proper orientation for the well established B-face-specific hydride transfer to C-4 from the corresponding substrate reaction center, crystallization data. The Lys171 residue lowers the pKa of the phenolic hydroxyl group of the Tyr167 in the catalytic triad together with the positively charged NAD+. The Ser153 residue then shares its proton with the phenolic anionic group of Tyr167, and in this way, the latter can serve as a general base in substrate deprotonation during catalysis. Concomitant deprotonation of the (-)-secoisolariciresinol is then presumed to occur via the phenolic anion of Tyr167 with hydride transfer to NAD+, followed by nucleophilic attack to form the (-)-lactol intermediate from (-)-secoisolariciresinol. Subsequent dehydrogenation of the (-)-lactol can then occur by the same process involving Tyr167 as before and a newly bound NAD+ molecule to afford the dibenzyl furanone, (-)-matairesinol	Podophyllum peltatum	(-)-matairesinol + 2 NADH + 2 H+	-	?

Cofactor

Cofactor	Comment	Organism	Structure
NADH	-	Podophyllum peltatum