Literature summary for 1.1.1.25 extracted from

Carrington, Y.; Guo, J.; Le, C.H.; Fillo, A.; Kwon, J.; Tran, L.T.; Ehlting, J.
Evolution of a secondary metabolic pathway from primary metabolism shikimate and quinate biosynthesis in plants (2018), Plant J., 95, 823-833 .

Search for more literature for 1.1.1.25

Cloned(Commentary)

Cloned (Comment)	Organism
gene SDH, phylogenetic analysis	Chlamydomonas reinhardtii
gene SDH, phylogenetic analysis	Pinus taeda
gene SDH, phylogenetic analysis	Physcomitrium patens
gene SDH, phylogenetic analysis	Rhodopirellula baltica
gene SDH, phylogenetic analysis	Selaginella moellendorffii
gene SDH1, phylogenetic analysis	Populus trichocarpa

Protein Variants

Protein Variants	Comment	Organism
S275G	site-directed mutagenesis, the mutant shows only slightly reduced maximum activity with shikimate compared with wild-type PoptrSDH1	Populus trichocarpa
S275G/T318G	site-directed mutagenesis, the double mutant is well expressed in Escherichia coli and shows bona fide QDH activity besides its original SDH activity, which is severely reduced. Although the Ser275Gly/Thr318Gly double mutant is clearly sufficient to confer gain of activity with quinate, its activity is lower than the QDH activities of PintaQDH and PoptrQDH2 activity	Populus trichocarpa
T318G	site-directed mutagenesis, the Thr318Gly mutant yields only a very small amount of enzyme when recombinantly expressed in Escherichia coli	Populus trichocarpa

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	Michaelis-Menten kinetics	Chlamydomonas reinhardtii
additional information	-	additional information	Michaelis-Menten kinetics	Pinus taeda
additional information	-	additional information	Michaelis-Menten kinetics	Physcomitrium patens
additional information	-	additional information	Michaelis-Menten kinetics	Populus trichocarpa
additional information	-	additional information	Michaelis-Menten kinetics	Rhodopirellula baltica
additional information	-	additional information	Michaelis-Menten kinetics	Selaginella moellendorffii
0.101	-	shikimate	pH and temperature not specified in the publication	Rhodopirellula baltica
0.12	-	shikimate	pH and temperature not specified in the publication	Chlamydomonas reinhardtii
0.218	-	shikimate	pH and temperature not specified in the publication	Pinus taeda
0.239	-	shikimate	pH and temperature not specified in the publication	Physcomitrium patens
0.279	-	shikimate	pH and temperature not specified in the publication	Selaginella moellendorffii
2.351	-	L-quinate	mutant S275G/T318G, pH and temperature not specified in the publication	Populus trichocarpa

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
shikimate + NAD+	Populus trichocarpa	the enzyme is also active with NAD+	3-dehydroshikimate + NADH + H+	-	r
shikimate + NADP+	Chlamydomonas reinhardtii	-	3-dehydroshikimate + NADPH + H+	-	r
shikimate + NADP+	Pinus taeda	-	3-dehydroshikimate + NADPH + H+	-	r
shikimate + NADP+	Physcomitrium patens	-	3-dehydroshikimate + NADPH + H+	-	r
shikimate + NADP+	Populus trichocarpa	-	3-dehydroshikimate + NADPH + H+	-	r
shikimate + NADP+	Rhodopirellula baltica	-	3-dehydroshikimate + NADPH + H+	-	r
shikimate + NADP+	Selaginella moellendorffii	-	3-dehydroshikimate + NADPH + H+	-	r

Organism

Organism	UniProt	Comment	Textmining
Chlamydomonas reinhardtii	-	-	-
Physcomitrium patens	-	-	-
Pinus taeda	-	-	-
Populus trichocarpa	-	-	-
Rhodopirellula baltica	-	-	-
Selaginella moellendorffii	-	-	-

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
91	-	mutant S275G, pH and temperature not specified in the publication	Populus trichocarpa
103	-	wild-type enzyme, pH and temperature not specified in the publication	Populus trichocarpa

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
L-quinate + NADP+	activity by only mutant S275G/T318G, not the wild-type enzyme	Populus trichocarpa	3-dehydroquinate + NADPH + H+	-	r
additional information	the wild-type enzyme PoptrSDH1 is highly shikimate-specific, only the S275G/T318G mutant shows activity with quinate	Populus trichocarpa	?	-	-
shikimate + NAD+	the enzyme is also active with NAD+	Populus trichocarpa	3-dehydroshikimate + NADH + H+	-	r
shikimate + NADP+	-	Chlamydomonas reinhardtii	3-dehydroshikimate + NADPH + H+	-	r
shikimate + NADP+	-	Pinus taeda	3-dehydroshikimate + NADPH + H+	-	r
shikimate + NADP+	-	Physcomitrium patens	3-dehydroshikimate + NADPH + H+	-	r
shikimate + NADP+	-	Populus trichocarpa	3-dehydroshikimate + NADPH + H+	-	r
shikimate + NADP+	-	Rhodopirellula baltica	3-dehydroshikimate + NADPH + H+	-	r
shikimate + NADP+	-	Selaginella moellendorffii	3-dehydroshikimate + NADPH + H+	-	r

Synonyms

Synonyms	Comment	Organism
ChlreSDH	-	Chlamydomonas reinhardtii
PhypaSDH	-	Physcomitrium patens
PintaSDH	-	Pinus taeda
PoptrSDH1	-	Populus trichocarpa
RhobaSDH	-	Rhodopirellula baltica
SDH	-	Chlamydomonas reinhardtii
SDH	-	Pinus taeda
SDH	-	Physcomitrium patens
SDH	-	Populus trichocarpa
SDH	-	Rhodopirellula baltica
SDH	-	Selaginella moellendorffii
SelmoSDH	-	Selaginella moellendorffii

Cofactor

Cofactor	Comment	Organism	Structure
NAD+	-	Populus trichocarpa
NADH	-	Populus trichocarpa
NADP+	-	Chlamydomonas reinhardtii
NADP+	-	Pinus taeda
NADP+	-	Physcomitrium patens
NADP+	-	Populus trichocarpa
NADP+	-	Rhodopirellula baltica
NADP+	-	Selaginella moellendorffii
NADPH	-	Chlamydomonas reinhardtii
NADPH	-	Pinus taeda
NADPH	-	Physcomitrium patens
NADPH	-	Populus trichocarpa
NADPH	-	Rhodopirellula baltica
NADPH	-	Selaginella moellendorffii

General Information

General Information	Comment	Organism
evolution	the enzyme belongs to the QDH family, phylogenetic reconstruction of the SDH/QDH gene family across land plants, overview. SDH and QDH belong to the same gene family, which diverged into two phylogenetic clades after a defining gene duplication just prior to the angiosperm/gymnosperm split. Non-seed plants that diverged before this duplication harbour only a single gene of this family. Extant representatives from the chlorophytes (Chlamydomonas reinhardtii), bryophytes (Physcomitrella patens) and lycophytes (Selaginella moellendorfii) encoded almost exclusively SDH activity in vitro. A reconstructed ancestral sequence representing the node just prior to the gene duplication also encoded SDH activity. Quinate dehydrogenase activity was gained only in seed plants following gene duplication. Quinate dehydrogenases of gymnosperms, e.g. Pinus taeda, may be reminiscent of an evolutionary intermediate since they encode equal SDH and QDH activities. The second copy in Pinus taeda maintains specificity for shikimate similar to the activity found in the angiosperm SDH sister clade. The codon for a tyrosine residue within the active site displays a signature of positive selection at the node defining the QDH clade, where it changed to a glycine. Replacing the tyrosine with a glycine in a highly shikimate-specific angiosperm SDH is sufficient to gain some QDH function. Thus, very few mutations are necessary to facilitate the evolution of QDH genes. The two proteins from Pinus taeda are chosen to represent the post-duplication SDH and QDH clades from gymnosperms. The single-copy genes from Selaginella moellendorffii, Physcomitrella patens and Chlamydomonas reinhardtii are selected to represent the pre-duplication lycopod, bryophyte and green algal clades, respectively. Thr381 is conserved in most members across all SDH clades but was replaced under positive selection by Gly in the branch leading into the seed plant QDH clade	Chlamydomonas reinhardtii
evolution	the enzyme belongs to the QDH family, phylogenetic reconstruction of the SDH/QDH gene family across land plants, overview. SDH and QDH belong to the same gene family, which diverged into two phylogenetic clades after a defining gene duplication just prior to the angiosperm/gymnosperm split. Non-seed plants that diverged before this duplication harbour only a single gene of this family. Extant representatives from the chlorophytes (Chlamydomonas reinhardtii), bryophytes (Physcomitrella patens) and lycophytes (Selaginella moellendorfii) encoded almost exclusively SDH activity in vitro. A reconstructed ancestral sequence representing the node just prior to the gene duplication also encoded SDH activity. Quinate dehydrogenase activity was gained only in seed plants following gene duplication. Quinate dehydrogenases of gymnosperms, e.g. Pinus taeda, may be reminiscent of an evolutionary intermediate since they encode equal SDH and QDH activities. The second copy in Pinus taeda maintains specificity for shikimate similar to the activity found in the angiosperm SDH sister clade. The codon for a tyrosine residue within the active site displays a signature of positive selection at the node defining the QDH clade, where it changed to a glycine. Replacing the tyrosine with a glycine in a highly shikimate-specific angiosperm SDH is sufficient to gain some QDH function. Thus, very few mutations are necessary to facilitate the evolution of QDH genes. The two proteins from Pinus taeda are chosen to represent the post-duplication SDH and QDH clades from gymnosperms. The single-copy genes from Selaginella moellendorffii, Physcomitrella patens and Chlamydomonas reinhardtii are selected to represent the pre-duplication lycopod, bryophyte and green algal clades, respectively. Thr381 is conserved in most members across all SDH clades but was replaced under positive selection by Gly in the branch leading into the seed plant QDH clade	Pinus taeda
evolution	the enzyme belongs to the QDH family, phylogenetic reconstruction of the SDH/QDH gene family across land plants, overview. SDH and QDH belong to the same gene family, which diverged into two phylogenetic clades after a defining gene duplication just prior to the angiosperm/gymnosperm split. Non-seed plants that diverged before this duplication harbour only a single gene of this family. Extant representatives from the chlorophytes (Chlamydomonas reinhardtii), bryophytes (Physcomitrella patens) and lycophytes (Selaginella moellendorfii) encoded almost exclusively SDH activity in vitro. A reconstructed ancestral sequence representing the node just prior to the gene duplication also encoded SDH activity. Quinate dehydrogenase activity was gained only in seed plants following gene duplication. Quinate dehydrogenases of gymnosperms, e.g. Pinus taeda, may be reminiscent of an evolutionary intermediate since they encode equal SDH and QDH activities. The second copy in Pinus taeda maintains specificity for shikimate similar to the activity found in the angiosperm SDH sister clade. The codon for a tyrosine residue within the active site displays a signature of positive selection at the node defining the QDH clade, where it changed to a glycine. Replacing the tyrosine with a glycine in a highly shikimate-specific angiosperm SDH is sufficient to gain some QDH function. Thus, very few mutations are necessary to facilitate the evolution of QDH genes. The two proteins from Pinus taeda are chosen to represent the post-duplication SDH and QDH clades from gymnosperms. The single-copy genes from Selaginella moellendorffii, Physcomitrella patens and Chlamydomonas reinhardtii are selected to represent the pre-duplication lycopod, bryophyte and green algal clades, respectively. Thr381 is conserved in most members across all SDH clades but was replaced under positive selection by Gly in the branch leading into the seed plant QDH clade	Physcomitrium patens
evolution	the enzyme belongs to the QDH family, phylogenetic reconstruction of the SDH/QDH gene family across land plants, overview. SDH and QDH belong to the same gene family, which diverged into two phylogenetic clades after a defining gene duplication just prior to the angiosperm/gymnosperm split. Non-seed plants that diverged before this duplication harbour only a single gene of this family. Extant representatives from the chlorophytes (Chlamydomonas reinhardtii), bryophytes (Physcomitrella patens) and lycophytes (Selaginella moellendorfii) encoded almost exclusively SDH activity in vitro. A reconstructed ancestral sequence representing the node just prior to the gene duplication also encoded SDH activity. Quinate dehydrogenase activity was gained only in seed plants following gene duplication. Quinate dehydrogenases of gymnosperms, e.g. Pinus taeda, may be reminiscent of an evolutionary intermediate since they encode equal SDH and QDH activities. The second copy in Pinus taeda maintains specificity for shikimate similar to the activity found in the angiosperm SDH sister clade. The codon for a tyrosine residue within the active site displays a signature of positive selection at the node defining the QDH clade, where it changed to a glycine. Replacing the tyrosine with a glycine in a highly shikimate-specific angiosperm SDH is sufficient to gain some QDH function. Thus, very few mutations are necessary to facilitate the evolution of QDH genes. The two proteins from Pinus taeda are chosen to represent the post-duplication SDH and QDH clades from gymnosperms. The single-copy genes from Selaginella moellendorffii, Physcomitrella patens and Chlamydomonas reinhardtii are selected to represent the pre-duplication lycopod, bryophyte and green algal clades, respectively. Thr381 is conserved in most members across all SDH clades but was replaced under positive selection by Gly in the branch leading into the seed plant QDH clade	Populus trichocarpa
evolution	the enzyme belongs to the QDH family, phylogenetic reconstruction of the SDH/QDH gene family across land plants, overview. SDH and QDH belong to the same gene family, which diverged into two phylogenetic clades after a defining gene duplication just prior to the angiosperm/gymnosperm split. Non-seed plants that diverged before this duplication harbour only a single gene of this family. Extant representatives from the chlorophytes (Chlamydomonas reinhardtii), bryophytes (Physcomitrella patens) and lycophytes (Selaginella moellendorfii) encoded almost exclusively SDH activity in vitro. A reconstructed ancestral sequence representing the node just prior to the gene duplication also encoded SDH activity. Quinate dehydrogenase activity was gained only in seed plants following gene duplication. Quinate dehydrogenases of gymnosperms, e.g. Pinus taeda, may be reminiscent of an evolutionary intermediate since they encode equal SDH and QDH activities. The second copy in Pinus taeda maintains specificity for shikimate similar to the activity found in the angiosperm SDH sister clade. The codon for a tyrosine residue within the active site displays a signature of positive selection at the node defining the QDH clade, where it changed to a glycine. Replacing the tyrosine with a glycine in a highly shikimate-specific angiosperm SDH is sufficient to gain some QDH function. Thus, very few mutations are necessary to facilitate the evolution of QDH genes. The two proteins from Pinus taeda are chosen to represent the post-duplication SDH and QDH clades from gymnosperms. The single-copy genes from Selaginella moellendorffii, Physcomitrella patens and Chlamydomonas reinhardtii are selected to represent the pre-duplication lycopod, bryophyte and green algal clades, respectively. Thr381 is conserved in most members across all SDH clades but was replaced under positive selection by Gly in the branch leading into the seed plant QDH clade	Rhodopirellula baltica
evolution	the enzyme belongs to the QDH family, phylogenetic reconstruction of the SDH/QDH gene family across land plants, overview. SDH and QDH belong to the same gene family, which diverged into two phylogenetic clades after a defining gene duplication just prior to the angiosperm/gymnosperm split. Non-seed plants that diverged before this duplication harbour only a single gene of this family. Extant representatives from the chlorophytes (Chlamydomonas reinhardtii), bryophytes (Physcomitrella patens) and lycophytes (Selaginella moellendorfii) encoded almost exclusively SDH activity in vitro. A reconstructed ancestral sequence representing the node just prior to the gene duplication also encoded SDH activity. Quinate dehydrogenase activity was gained only in seed plants following gene duplication. Quinate dehydrogenases of gymnosperms, e.g. Pinus taeda, may be reminiscent of an evolutionary intermediate since they encode equal SDH and QDH activities. The second copy in Pinus taeda maintains specificity for shikimate similar to the activity found in the angiosperm SDH sister clade. The codon for a tyrosine residue within the active site displays a signature of positive selection at the node defining the QDH clade, where it changed to a glycine. Replacing the tyrosine with a glycine in a highly shikimate-specific angiosperm SDH is sufficient to gain some QDH function. Thus, very few mutations are necessary to facilitate the evolution of QDH genes. The two proteins from Pinus taeda are chosen to represent the post-duplication SDH and QDH clades from gymnosperms. The single-copy genes from Selaginella moellendorffii, Physcomitrella patens and Chlamydomonas reinhardtii are selected to represent the pre-duplication lycopod, bryophyte and green algal clades, respectively. Thr381 is conserved in most members across all SDH clades but was replaced under positive selection by Gly in the branch leading into the seed plant QDH clade	Selaginella moellendorffii
metabolism	link between reactions catalysed by the shikimate pathway enzyme dehydroquinate dehydratase (DQD)/shikimate dehydrogenase (SDH) and quinate dehydrogenase (QDH) involved in quinate metabolism. Shikimate is produced from dehydroquinate via a two-step reaction and subsequently channelled to downstream reactions in the pathway. Quinate is reversibly formed from a side branch of the shikimate pathway from dehydroquinate and may be converted to more structurally complex secondary metabolites or to dehydroquinate to fuel the shikimate pathway	Chlamydomonas reinhardtii
metabolism	link between reactions catalysed by the shikimate pathway enzyme dehydroquinate dehydratase (DQD)/shikimate dehydrogenase (SDH) and quinate dehydrogenase (QDH) involved in quinate metabolism. Shikimate is produced from dehydroquinate via a two-step reaction and subsequently channelled to downstream reactions in the pathway. Quinate is reversibly formed from a side branch of the shikimate pathway from dehydroquinate and may be converted to more structurally complex secondary metabolites or to dehydroquinate to fuel the shikimate pathway	Pinus taeda
metabolism	link between reactions catalysed by the shikimate pathway enzyme dehydroquinate dehydratase (DQD)/shikimate dehydrogenase (SDH) and quinate dehydrogenase (QDH) involved in quinate metabolism. Shikimate is produced from dehydroquinate via a two-step reaction and subsequently channelled to downstream reactions in the pathway. Quinate is reversibly formed from a side branch of the shikimate pathway from dehydroquinate and may be converted to more structurally complex secondary metabolites or to dehydroquinate to fuel the shikimate pathway	Physcomitrium patens
metabolism	link between reactions catalysed by the shikimate pathway enzyme dehydroquinate dehydratase (DQD)/shikimate dehydrogenase (SDH) and quinate dehydrogenase (QDH) involved in quinate metabolism. Shikimate is produced from dehydroquinate via a two-step reaction and subsequently channelled to downstream reactions in the pathway. Quinate is reversibly formed from a side branch of the shikimate pathway from dehydroquinate and may be converted to more structurally complex secondary metabolites or to dehydroquinate to fuel the shikimate pathway	Populus trichocarpa
metabolism	link between reactions catalysed by the shikimate pathway enzyme dehydroquinate dehydratase (DQD)/shikimate dehydrogenase (SDH) and quinate dehydrogenase (QDH) involved in quinate metabolism. Shikimate is produced from dehydroquinate via a two-step reaction and subsequently channelled to downstream reactions in the pathway. Quinate is reversibly formed from a side branch of the shikimate pathway from dehydroquinate and may be converted to more structurally complex secondary metabolites or to dehydroquinate to fuel the shikimate pathway	Rhodopirellula baltica
metabolism	link between reactions catalysed by the shikimate pathway enzyme dehydroquinate dehydratase (DQD)/shikimate dehydrogenase (SDH) and quinate dehydrogenase (QDH) involved in quinate metabolism. Shikimate is produced from dehydroquinate via a two-step reaction and subsequently channelled to downstream reactions in the pathway. Quinate is reversibly formed from a side branch of the shikimate pathway from dehydroquinate and may be converted to more structurally complex secondary metabolites or to dehydroquinate to fuel the shikimate pathway	Selaginella moellendorffii

Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.

Release 2023.1 (January 2023)