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