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Information on EC 1.1.1.331 - secoisolariciresinol dehydrogenase
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1.1.1.331 secoisolariciresinol dehydrogenaseIUBMB Comments
Isolated from the plants Forsythia intermedia and Podophyllum peltatum [1-3]. An intermediate lactol is detected in vitro.
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Word Map
- 1.1.1.331
-
lignans
- podophyllum
- forsythia
- podophyllotoxin
- enterolactone
- plr
- intermedia
- peltatum
- teniposide
-
enantiospecific
- etoposide
- rhizome
-
phytoestrogens
- glucosides
-
semi-synthetic
- enterodiol
-
cancer-preventative
- koreana
-
bioconversion
- callus
- linum
- versipellis
- hexandrum
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Synonyms
FkSIRD, matairesinol biosynthetic enzyme, PhSDH, PpSD, SDH, sdh-PpH, SDH_Pp7, secoisolariciresinol dehydrogenase, SirD, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
SDH
secoisolariciresinol dehydrogenase
SirD
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(-)-secoisolariciresinol + 2 NAD+ = (-)-matairesinol + 2 NADH + 2 H+
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
(-)-secoisolariciresinol:NAD+ oxidoreductase
Isolated from the plants Forsythia intermedia [1] and Podophyllum peltatum [1-3]. An intermediate lactol is detected in vitro.
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CAS REGISTRY NUMBER
COMMENTARY
249765-11-5
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
product is optically pure, more than 99% enantiomeric excess. (-)-Matairesinol is formed preferentially in the in vitro reactions with enzyme preparations. The opposite (+)-enantiomer is isolated from Daphne genkwa shoot
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
product is optically pure, more than 99% enantiomeric excess. (-)-Matairesinol is formed preferentially in the in vitro reactions with enzyme preparations. The opposite (+)-enantiomer is isolated from Daphne odora callus
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
conversion is enantiospecific, reaction proceeds via the corresponding lactol intermediate
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
Phialocephala podophylli
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
Phialocephala podophylli PPE7
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
conversion is enantiospecific, reaction proceeds via the corresponding lactol intermediate
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
NAD+ binds first followed by the substrate (-)-secoisolariciresinol. For hydride transfer, the incoming hydride abstracted from the substrate takes up the pro-S position in the NADH formed
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
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
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
Phialocephala podophylli
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
Phialocephala podophylli PPE7
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
-
?
(-)-secoisolariciresinol + 2 NAD+
(-)-matairesinol + 2 NADH + 2 H+
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.231
(-)-secoisolariciresinol
pH 8.8, 20°C, recombinant His-tagged enzyme
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.8
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Phialocephala podophylli
isolated from the rhizomes of Podophyllum peltatum
UniProt
brenda
Phialocephala podophylli PPE7
isolated from the rhizomes of Podophyllum peltatum
UniProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
seasonal alteration in amounts of major lignans, such as pinoresinol, matairesinol, and arctigenin, analysis of gene expression profile of secoisolariciresinol dehydrogenase (SIRD) and other related enzymes in the leaves of Forsythia suspense from April to November. The SIRD expression is prominent from April to May, not detected in June to July, and then increases again from September to November. All of the lignans in the leaf continuously increase from April to June, reach the maximal level in June, and then decrease
brenda
additional information
no expression detected in leaf and flower. The expression levels of enzyme are not consistent with the amounts of podophyllotxin in the tissues tested
brenda
additional information
-
tissue- and species-specific expression of the lignan biosynthesis-related gene FkSIRD, transcriptome analysis, overview. The expression levels of DIR, PLR, SIRD, and MOMT are 40fold, 5fold, 50fold, and 2fold higher in callus than in leaf, respectively
brenda
additional information
expression pattern of PhSDH in different tissues and under abiotic stress, overview. PhSDH has the lowest expression in leaf compared to stem and root
brenda
additional information
-
expression pattern of PhSDH in different tissues and under abiotic stress, overview. PhSDH has the lowest expression in leaf compared to stem and root
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
-
molecular phylogenetic analysis of specialized metabolic enzyme genes from lignan-producing plants, two common gene clusters include genes from various plants and plant lineage-specific gene clusters. The specialized metabolic enzyme genes from lignan-producing plants include enzymes involved in the early common lignan biosynthesis upstream of matairesinol such as PLR and SIRD, suggesting that they have occurred in their ancestral plants and conserved their biological functions
metabolism
physiological function
additional information
metabolism
-
the enzyme is involved in the lignan biosynthesis pathway, overview
metabolism
the enzyme is involved in the lignan biosynthetic pathways in Forsythia, overview
metabolism
the enzyme is part of the podophyllotoxin, PPT, biosynthetic pathway
metabolism
Phialocephala podophylli
the enzyme is part of the podophyllotoxin, PPT, biosynthetic pathway
metabolism
the enzyme is part of the podophyllotoxin, PPT, biosynthetic pathway, overview. Podophyllotoxin is an important aryltetralin lignan, that possesses antitumor and antihyperlipidemic activities
metabolism
Phialocephala podophylli PPE7
-
the enzyme is part of the podophyllotoxin, PPT, biosynthetic pathway
-
physiological function
-
matairesinol biosynthesis is prominently enhanced and matairesinol is highly accumulated in callus
physiological function
the enzyme secoisolariciresinol dehydrogenase facilitates the dehydrogenation of secoisolariciresinol to form matairesinol, a mid-pathway intermediate product in podophyllotoxin, PPT, biosynthesis
physiological function
Phialocephala podophylli
the enzyme secoisolariciresinol dehydrogenase facilitates the dehydrogenation of secoisolariciresinol to form matairesinol, a mid-pathway intermediate product in podophyllotoxin, PPT, biosynthesis
physiological function
the enzyme SIRD is involved in the biosynthesis of lignan matairesinol in Forsythia. The leaves show seasonal alteration in amounts of major lignans, such as pinoresinol, matairesinol, and arctigenin, gene expression profile of secoisolariciresinol dehydrogenase (SIRD) and other related enzymes in the leaves of Forsythia suspense from April to November: all of the lignans in the leaf continuously increase from April to June, reach the maximal level in June, and then decrease
physiological function
Phialocephala podophylli PPE7
-
the enzyme secoisolariciresinol dehydrogenase facilitates the dehydrogenation of secoisolariciresinol to form matairesinol, a mid-pathway intermediate product in podophyllotoxin, PPT, biosynthesis
-
additional information
the enzyme forms a homotetramer composed of an alpha/beta single domain structure with a dinucleotide-binding Rossmann fold for the binding of NAD+ and an active site with a highly conserved catalytic triad of amino acids, Ser153, Tyr167 and Lys171
additional information
-
the enzyme forms a homotetramer composed of an alpha/beta single domain structure with a dinucleotide-binding Rossmann fold for the binding of NAD+ and an active site with a highly conserved catalytic triad of amino acids, Ser153, Tyr167 and Lys171
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). SDH_SINHE
278
0
29196
Swiss-Prot
other Location (Reliability: 2)
SILD_FORIN
277
0
29256
Swiss-Prot
other Location (Reliability: 5)
SILD_FORIN
277
0
29256
Swiss-Prot
other Location (Reliability: 5)
SILD_PODPE
278
0
29253
Swiss-Prot
other Location (Reliability: 1)
A0A396I950_MEDTR
274
0
28804
TrEMBL
other Location (Reliability: 3)
A0A2P6RCB9_ROSCH
285
0
29982
TrEMBL
other Location (Reliability: 2)
A0A2P6RCC2_ROSCH
278
0
29496
TrEMBL
other Location (Reliability: 4)
A0A396H639_MEDTR
244
0
25848
TrEMBL
Secretory Pathway (Reliability: 2)
A0A2P6QKT3_ROSCH
74
0
7752
TrEMBL
other Location (Reliability: 5)
A0A2G9G0R9_9LAMI
281
0
29710
TrEMBL
other Location (Reliability: 3)
A0A396IH17_MEDTR
181
0
19148
TrEMBL
other Location (Reliability: 2)
A0A072U384_MEDTR
195
0
20692
TrEMBL
other Location (Reliability: 3)
A0A396H876_MEDTR
268
0
28391
TrEMBL
other Location (Reliability: 3)
A0A396H661_MEDTR
255
0
27286
TrEMBL
other Location (Reliability: 3)
A0A2P6QE97_ROSCH
270
0
28554
TrEMBL
Mitochondrion (Reliability: 4)
A0A396H7G5_MEDTR
274
0
28820
TrEMBL
other Location (Reliability: 3)
A0A2G9I8H6_9LAMI
293
0
31179
TrEMBL
Mitochondrion (Reliability: 2)
A0A396IBJ7_MEDTR
273
0
29218
TrEMBL
other Location (Reliability: 4)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
32000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
?
x * 34000, recombinant His-tagged enzyme, SDS-PAGE, x * 65000, recombinant His-tagged fusion enzyme PLR-SDH , SDS-PAGE
additional information
the enzyme forms a homotetramer composed of an alpha/beta single domain structure with a dinucleotide-binding Rossmann fold for the binding of NAD+ and an active site with a highly conserved catalytic triad of amino acids, Ser153, Tyr167 and Lys171
additional information
-
the enzyme forms a homotetramer composed of an alpha/beta single domain structure with a dinucleotide-binding Rossmann fold for the binding of NAD+ and an active site with a highly conserved catalytic triad of amino acids, Ser153, Tyr167 and Lys171
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K171A
mutation in conserved catalytic triad, complete loss of activity
S153A
mutation in conserved catalytic triad, severe reduction of activity
Y167A
mutation in conserved catalytic triad, complete loss of activity
additional information
additional information
the two genes, termed plr-PpH and sdh-PpH, encoding pinoresinol-lariciresinol reductase (PLR) and secoisolariciresinol dehydrogenase (SDH), are linked to form two bifunctional fusion genes, plr-sdh and sdh-plr, which are expressed in Escherichia coli and purified. The proteins are linked via a (GGGGS)4 protein linker to maintain flexibility. Bioconversion in vitro at 22°C for 60 min shows that the conversion efficiency of fusion protein PLR-SDH is higher than that of the mixture of recombinant PLR and reacombinant SDH. The percent conversion of (+)-pinoresinol to matairesinol is 49.8% using PLR-SDH and only 17.7% using a mixture of rPLR and rSDH. Conversion of (+)-pinoresinol by fusion protein SDH-PLR stops at the intermediate product, secoisolariciresinol. In vivo, (+)-pinoresinol is completely converted to matairesinol by living recombinant Escherichia coli expressing PLR-SDH without addition of cofactors
additional information
-
the two genes, termed plr-PpH and sdh-PpH, encoding pinoresinol-lariciresinol reductase (PLR) and secoisolariciresinol dehydrogenase (SDH), are linked to form two bifunctional fusion genes, plr-sdh and sdh-plr, which are expressed in Escherichia coli and purified. The proteins are linked via a (GGGGS)4 protein linker to maintain flexibility. Bioconversion in vitro at 22°C for 60 min shows that the conversion efficiency of fusion protein PLR-SDH is higher than that of the mixture of recombinant PLR and reacombinant SDH. The percent conversion of (+)-pinoresinol to matairesinol is 49.8% using PLR-SDH and only 17.7% using a mixture of rPLR and rSDH. Conversion of (+)-pinoresinol by fusion protein SDH-PLR stops at the intermediate product, secoisolariciresinol. In vivo, (+)-pinoresinol is completely converted to matairesinol by living recombinant Escherichia coli expressing PLR-SDH without addition of cofactors
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme SDH and bifunctional fusion enzyme PLR-SDH from Escherichia coli
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, sequence comparisons, cloning and expression in Escherichiaa coli strain JM109. Confirmation that the SD gene sequence originates from Phialocephala podophylli strain PPE7 fungal gDNA and is not a product from amplification of Podophyllum peltatum gDNA plant contamination is achieved through PCR amplification of any contaminating rbcL plant gene sequences in the PPE7 fungal gDNA template samples
Phialocephala podophylli
expression in Escherichia coli
gene FkSIRD, DNA and amino acid sequence determination and analysis from Forsythia genome, phylogenetic analysis, quantitative RT-PCR enzyme expression analysis
-
gene PhSDH, sequence comparisons, semiquantitative RT-PCR expression analysis
gene sdh-PpH, DNA and amino acid sequence determination and analysis, sequence comparisons, recombinant expression of His-tagged enzyme in Escherichia coli strain M15. Genes plr-PpH, encoding pinoresinol-lariciresinol reductase (PLR), and sdh-PpH are linked to form two bifunctional fusion genes, plr-sdh and sdh-plr, which are expressed as functional His-tagged proteins in Escherichia coli strain M15. Establishment of a high-efficiency system for the conversion of (+)-pinoresinol to (-)-matairesinol in Escherichia coli expressing a Sdh-PpH fusion protein
gene SDH_Pp7, DNA and amino acid sequence determination and analysis, sequence comparisons, cloning and expression in Escherichia coli strain JM109, compatible codon optimization for expression in the heterologous host Pichia pastoris
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
all of the enzymes responsible for the biosynthesis of lignan aglycones, also SIRD, are upregulated in callus
-
the enzyme expression is induced by wounding and methyl jasmonate, while UV light induces short peaks of the enzyme expression after 6 h intervals, expression pattern of PhSDH in different tissues and under abiotic stress, overview
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Xia, Z.Q.; Costa, M.A.; Pelissier, H.C.; Davin, L.B.; Lewis, N.G.
Secoisolariciresinol dehydrogenase purification, cloning, and functional expression. Implications for human health protection
J. Biol. Chem.
276
12614-12623
2001
Forsythia x intermedia (Q94KL7), Forsythia x intermedia, Podophyllum peltatum (Q94KL8), Podophyllum peltatum
brenda
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
J. Biol. Chem.
280
12917-12926
2005
Podophyllum peltatum (Q94KL8)
brenda
Lan, X.; Ren, S.; Yang, Y.; Chen, M.; Yang, C.; Quan, H.; Zhong, G.; Liao, Z.
Molecular cloning and characterization of the secoisolariciresinol dehydrogenase gene involved in podophyllotoxin biosynthetic pathway from Tibet Dysosma
J. Med. Plant Res.
4
484-489
2010
Dysosma tsayuensis (Q1ZZ69)
-
brenda
Okunishi, T.; Sakakibara, N.; Suzuki, S.; Umezawa, T.; Shimada, M.
Stereochemistry of matairesinol formation by Daphne secoisolariciresinol dehydrogenase
J. Wood Sci.
50
77-81
2004
Daphne odora, Daphne genkwa
-
brenda
Moinuddin, S.G.; Youn, B.; Bedgar, D.L.; Costa, M.A.; Helms, G.L.; Kang, C.; Davin, L.B.; Lewis, N.G.
Secoisolariciresinol dehydrogenase: mode of catalysis and stereospecificity of hydride transfer in Podophyllum peltatum
Org. Biomol. Chem.
4
808-816
2006
Podophyllum peltatum (Q94KL8), Podophyllum peltatum
brenda
Kuo, H.J.; Wei, Z.Y.; Lu, P.C.; Huang, P.L.; Lee, K.T.
Bioconversion of pinoresinol into matairesinol by use of recombinant Escherichia coli
Appl. Environ. Microbiol.
80
2687-2692
2014
Dysosma pleiantha (W8NQ72), Dysosma pleiantha
brenda
Morimoto, K.; Satake, H.
Seasonal alteration in amounts of lignans and their glucosides and gene expression of the relevant biosynthetic enzymes in the Forsythia suspense leaf
Biol. Pharm. Bull.
36
1519-1523
2013
Forsythia x intermedia (Q94KL7)
brenda
Arneaud, S.L.; Porter, J.R.
Investigation and expression of the secoisolariciresinol dehydrogenase gene involved in podophyllotoxin biosynthesis
Mol. Biotechnol.
57
961-973
2015
Podophyllum peltatum (A0A0M4J2R3), Podophyllum peltatum, Phialocephala podophylli (A0A0M5K823), Phialocephala podophylli PPE7 (A0A0M5K823)
brenda
Shiraishi, A.; Murata, J.; Matsumoto, E.; Matsubara, S.; Ono, E.; Satake, H.
De novo transcriptomes of Forsythia koreana using a novel assembly method insight into tissue- and species-specific expression of lignan biosynthesis-related gene
PLoS ONE
11
e0164805
2016
Forsythia koreana
brenda
Wankhede, D.P.; Biswas, D.K.; Rajkumar, S.; Sinha, A.K.
Expressed sequence tags and molecular cloning and characterization of gene encoding pinoresinol/lariciresinol reductase from Podophyllum hexandrum
Protoplasma
250
1239-1249
2013
Sinopodophyllum hexandrum (A3F5F0), Sinopodophyllum hexandrum
brenda
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