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. 2018 Oct 4;8(1):14796.
doi: 10.1038/s41598-018-32967-1.

A multisubstrate reductase from Plantago major: structure-function in the short chain reductase superfamily

Affiliations

A multisubstrate reductase from Plantago major: structure-function in the short chain reductase superfamily

Rachel Fellows et al. Sci Rep. .

Abstract

The short chain dehydrogenase/reductase superfamily (SDR) is a large family of NAD(P)H-dependent enzymes found in all kingdoms of life. SDRs are particularly well-represented in plants, playing diverse roles in both primary and secondary metabolism. In addition, some plant SDRs are also able to catalyse a reductive cyclisation reaction critical for the biosynthesis of the iridoid backbone that contains a fused 5 and 6-membered ring scaffold. Mining the EST database of Plantago major, a medicinal plant that makes iridoids, we identified a putative 5β-progesterone reductase gene, PmMOR (P. major multisubstrate oxido-reductase), that is 60% identical to the iridoid synthase gene from Catharanthus roseus. The PmMOR protein was recombinantly expressed and its enzymatic activity assayed against three putative substrates, 8-oxogeranial, citral and progesterone. The enzyme demonstrated promiscuous enzymatic activity and was able to not only reduce progesterone and citral, but also to catalyse the reductive cyclisation of 8-oxogeranial. The crystal structures of PmMOR wild type and PmMOR mutants in complex with NADP+ or NAD+ and either 8-oxogeranial, citral or progesterone help to reveal the substrate specificity determinants and catalytic machinery of the protein. Site-directed mutagenesis studies were performed and provide a foundation for understanding the promiscuous activity of the enzyme.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
PRISE family reduction reactions. (A) Substrates and products for NADPH-dependent reduction reactions for PmMOR, CrIS and Dl5ß –POR. (i) Reductive cyclisation reaction of 8-oxogeranial postulated for CrIS and PmMOR. (ii) Double bond reduction reaction at the 5-position of the A ring of progesterone catalyzed by Dl5ß –POR. (iii) Reduction of the aldehyde (top) and alkene (bottom) of citral by PmMOR yielding alcohol and reduced products. (B) 1H NMR spectrum of an overnight reaction of PmMOR with NADPH and 8-oxogeranial. The chemical shifts and coupling patterns correspond to the starting material, 8-oxogeranial or nepetalactol and are indicated.
Figure 2
Figure 2
Overall fold of PmMOR. (A) PmMOR dimer shown as cartoon and colored as rainbow from N (blue) to C (red)-terminus, termini are labeled. Residues involved in dimerisation are labeled, shown as sticks and colored by atom with carbons in cyan. (B) PmMOR cartoon bound with NADP+ and 8-oxogeranial shown as sticks with carbons in cyan and colored by atom. The capping domain is shown in blue and the Rossmann domain in red. Domains and substrate binding pocket are indicated with arrows and termini are labeled.
Figure 3
Figure 3
Active site close-up of PmMOR bound with NADP+ and 8-oxogeranial and sequence alignment of PmMOR, CrIS and Dl5ß-POR. (A) NADP+ binding residues depicted as sticks. Residues are labeled and hydrogen bonding interactions are depicted as dotted blue lines with the distances between atoms given. The cofactor binding site is formed primarily by the Rossmann fold domain. Residues ILE-206, MET-215 and SER-213 from the helical cap domain help to sequester the cofactor. (B) 8-oxogeranial binding site labeled as per (A). The distance between the reactive hydride and the substrate is 7.1 Å, non-optimum for catalysis. (C) Sequence alignment of P. major multifunctional oxido-reductase (PmMOR), D. lanata 5-ß progesterone oxido-reductase (Dl5ß-POR) and C. roseus iridoid synthase (CrIS). Approximately every tenth position is marked with an asterisk. Putative catalytic residues are highlighted in cyan and active site mutants are highlighted in yellow. The loop region that differs in orientation between PmMOR and CrIS corresponding to residues 349–354 is underlined.
Figure 4
Figure 4
Ligand binding pocket comparison. (A) Close-up view of the 8-oxogeranial binding site of PmMOR (carbons colored cyan) overlaid with 5DF1 (CrIS with NADP+ and geranic acid with carbons colored gray) and 5DBI (CrIS with NADP+ and 8-oxogeranial with carbons colored purple). Residues are labeled as per PmMOR numbering except LEU-203, which corresponds to CrIS. 8-oxogeranial is shifted away from the NADP+ in PmMOR versus CrIS. (B) Active site view highlighting the shifted loop between PmMOR (dark blue) and CrIS (dark and light green). The 349-DIPCPL-354 loop is indicated with black arrows. (C) Omit map contoured at +3.5 standard deviations (σ) above the mean shown in green mesh for the PmMOR/NADP+/8-oxogeranial structure. Selected side chain residues are drawn as sticks and labeled.
Figure 5
Figure 5
PmMORV150M citral binding. (A) Close-up view of the active site showing putative catalytic residues for citral with distances shown as blue dashed lines and labeled. The two citral conformations are show with carbons in cyan and green. Omit map contoured at +3.5 standard deviations (σ) above the mean shown in green mesh. (B) A cutaway of the PmMOR active site is shown with the two citral binding modes colored as per A. Selected residues are labeled.
Figure 6
Figure 6
PmMORV150M progesterone binding. (A) Stereo-view of the active site of PmMORV150M in complex with NADP+ and progesterone with protein and side chains shown in gray. Selected residues near the ligand are shown in sticks. NADP+ is colored by atom with carbons in gray. Progesterone is colored by atom with carbons in cyan. The binding mode of progesterone postulated by Thorn, et al. is shown and colored by atom with carbons in gray. Note the steric clash with ASN-205 for this binding mode. Distances between the reactive hydride and carbon-carbon double bond to be reduced are 6.3 Å and 7.1 Å for the PmMOR and Thorn, et al. conformation, respectively. (B) PmMORV150M progesterone omit map contoured at +3.5 standard deviations (σ) above the mean shown in green mesh. Selected side chain residues are drawn as sticks and labeled. The PmMORWT progesterone ligand is shown in yellow sticks and the PmMORV150M progesterone is shown in cyan sticks.

References

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