Literature summary 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 .

Cloned(Commentary)

EC Number	Cloned (Comment)	Organism
1.1.1.24	gene QDH2, phylogenetic analysis	Populus trichocarpa
1.1.1.25	gene SDH, phylogenetic analysis	Chlamydomonas reinhardtii
1.1.1.25	gene SDH, phylogenetic analysis	Pinus taeda
1.1.1.25	gene SDH, phylogenetic analysis	Physcomitrium patens
1.1.1.25	gene SDH, phylogenetic analysis	Rhodopirellula baltica
1.1.1.25	gene SDH, phylogenetic analysis	Selaginella moellendorffii
1.1.1.25	gene SDH1, phylogenetic analysis	Populus trichocarpa
1.1.1.282	gene PintaQDH, detailed phylogenetic analysis and tree	Pinus taeda

Protein Variants

EC Number	Protein Variants	Comment	Organism
1.1.1.25	S275G	site-directed mutagenesis, the mutant shows only slightly reduced maximum activity with shikimate compared with wild-type PoptrSDH1	Populus trichocarpa
1.1.1.25	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
1.1.1.25	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]

EC Number	KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
1.1.1.24	additional information	-	additional information	Michaelis-Menten kinetics	Populus trichocarpa
1.1.1.25	additional information	-	additional information	Michaelis-Menten kinetics	Chlamydomonas reinhardtii
1.1.1.25	additional information	-	additional information	Michaelis-Menten kinetics	Pinus taeda
1.1.1.25	additional information	-	additional information	Michaelis-Menten kinetics	Physcomitrium patens
1.1.1.25	additional information	-	additional information	Michaelis-Menten kinetics	Populus trichocarpa
1.1.1.25	additional information	-	additional information	Michaelis-Menten kinetics	Rhodopirellula baltica
1.1.1.25	additional information	-	additional information	Michaelis-Menten kinetics	Selaginella moellendorffii
1.1.1.25	0.101	-	shikimate	pH and temperature not specified in the publication	Rhodopirellula baltica
1.1.1.25	0.12	-	shikimate	pH and temperature not specified in the publication	Chlamydomonas reinhardtii
1.1.1.25	0.218	-	shikimate	pH and temperature not specified in the publication	Pinus taeda
1.1.1.25	0.239	-	shikimate	pH and temperature not specified in the publication	Physcomitrium patens
1.1.1.25	0.279	-	shikimate	pH and temperature not specified in the publication	Selaginella moellendorffii
1.1.1.25	2.351	-	L-quinate	mutant S275G/T318G, pH and temperature not specified in the publication	Populus trichocarpa
1.1.1.282	additional information	-	additional information	Michaelis-Menten kinetics	Pinus taeda
1.1.1.282	0.677	-	L-quinate	pH and temperature not specified in the publication, enzyme PintaQDH with NADP+	Pinus taeda
1.1.1.282	0.82	-	shikimate	pH and temperature not specified in the publication, enzyme PintaQDH with NADP+	Pinus taeda

Natural Substrates/ Products (Substrates)

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

Organism

EC Number	Organism	UniProt	Comment	Textmining
1.1.1.24	Populus trichocarpa	-	-	-
1.1.1.25	Chlamydomonas reinhardtii	-	-	-
1.1.1.25	Physcomitrium patens	-	-	-
1.1.1.25	Pinus taeda	-	-	-
1.1.1.25	Populus trichocarpa	-	-	-
1.1.1.25	Rhodopirellula baltica	-	-	-
1.1.1.25	Selaginella moellendorffii	-	-	-
1.1.1.282	Pinus taeda	-	-	-

Specific Activity [micromol/min/mg]

EC Number	Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
1.1.1.25	91	-	mutant S275G, pH and temperature not specified in the publication	Populus trichocarpa
1.1.1.25	103	-	wild-type enzyme, pH and temperature not specified in the publication	Populus trichocarpa

Substrates and Products (Substrate)

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

Synonyms

EC Number	Synonyms	Comment	Organism
1.1.1.24	PoptrQDH2	-	Populus trichocarpa
1.1.1.24	QDH	-	Populus trichocarpa
1.1.1.24	QDH2	-	Populus trichocarpa
1.1.1.25	ChlreSDH	-	Chlamydomonas reinhardtii
1.1.1.25	PhypaSDH	-	Physcomitrium patens
1.1.1.25	PintaSDH	-	Pinus taeda
1.1.1.25	PoptrSDH1	-	Populus trichocarpa
1.1.1.25	RhobaSDH	-	Rhodopirellula baltica
1.1.1.25	SDH	-	Chlamydomonas reinhardtii
1.1.1.25	SDH	-	Pinus taeda
1.1.1.25	SDH	-	Physcomitrium patens
1.1.1.25	SDH	-	Populus trichocarpa
1.1.1.25	SDH	-	Rhodopirellula baltica
1.1.1.25	SDH	-	Selaginella moellendorffii
1.1.1.25	SelmoSDH	-	Selaginella moellendorffii
1.1.1.282	PintaQDH	-	Pinus taeda
1.1.1.282	QDH	-	Pinus taeda

Cofactor

EC Number	Cofactor	Comment	Organism
1.1.1.24	NAD+	-	Populus trichocarpa
1.1.1.24	NADH	-	Populus trichocarpa
1.1.1.25	NAD+	-	Populus trichocarpa
1.1.1.25	NADH	-	Populus trichocarpa
1.1.1.25	NADP+	-	Chlamydomonas reinhardtii
1.1.1.25	NADP+	-	Pinus taeda
1.1.1.25	NADP+	-	Physcomitrium patens
1.1.1.25	NADP+	-	Populus trichocarpa
1.1.1.25	NADP+	-	Rhodopirellula baltica
1.1.1.25	NADP+	-	Selaginella moellendorffii
1.1.1.25	NADPH	-	Chlamydomonas reinhardtii
1.1.1.25	NADPH	-	Pinus taeda
1.1.1.25	NADPH	-	Physcomitrium patens
1.1.1.25	NADPH	-	Populus trichocarpa
1.1.1.25	NADPH	-	Rhodopirellula baltica
1.1.1.25	NADPH	-	Selaginella moellendorffii
1.1.1.282	NAD+	-	Pinus taeda
1.1.1.282	NADH	-	Pinus taeda
1.1.1.282	NADP+	-	Pinus taeda
1.1.1.282	NADPH	-	Pinus taeda

General Information

EC Number	General Information	Comment	Organism
1.1.1.24	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
1.1.1.24	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
1.1.1.25	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
1.1.1.25	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
1.1.1.25	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
1.1.1.25	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
1.1.1.25	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
1.1.1.25	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
1.1.1.25	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
1.1.1.25	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
1.1.1.25	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
1.1.1.25	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
1.1.1.25	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
1.1.1.25	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
1.1.1.282	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
1.1.1.282	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