BRENDA - Enzyme Database

Evolution of a new chlorophyll metabolic pathway driven by the dynamic changes in enzyme promiscuous activity

Ito, H.; Tanaka, A.; Plant Cell Physiol. 55, 593-603 (2014)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
1.3.1.75
gene DVR, phylogenetic analysis
Arabidopsis thaliana
1.3.1.75
gene DVR, phylogenetic analysis, recombinant expression of NADPH-dependent DVR in Escherichia coli
Phaeodactylum tricornutum
1.3.7.13
gene slr1923, phylogenetic analysis
Synechocystis sp. PCC 6803
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.3.1.75
3,8-divinyl chlorophyll a + NADPH + H+
Phaeodactylum tricornutum
very low activity
chlorophyll a + NADP+
-
-
?
1.3.1.75
3,8-divinyl chlorophyllide a + NADPH + H+
Phaeodactylum tricornutum
-
chlorophyllide a + NADP+
-
-
?
1.3.1.75
3,8-divinyl chlorophyllide a + NADPH + H+
Arabidopsis thaliana
low activity
chlorophyllide a + NADP+
-
-
?
1.3.7.13
3,8-divinyl chlorophyll a + reduced ferredoxin [iron-sulfur] cluster + H+
Synechocystis sp. PCC 6803
-
chlorophyll a + oxidized ferredoxin [iron-sulfur] cluster
-
-
?
1.3.7.13
3,8-divinyl chlorophyllide a + reduced ferredoxin [iron-sulfur] cluster + H+
Synechocystis sp. PCC 6803
-
chlorophyllide a + oxidized ferredoxin [iron-sulfur] cluster
-
-
?
1.3.7.13
3,8-divinyl protochlorophyllide a + reduced ferredoxin [iron-sulfur] cluster + H+
Synechocystis sp. PCC 6803
-
protochlorophyllide a + oxidized ferredoxin [iron-sulfur] cluster
-
-
?
1.3.7.13
additional information
Synechocystis sp. PCC 6803
cyanobacterial 3,8-divinyl chlorophyllide reductase (DVR) is a Chl biosynthetic enzyme that has many promiscuous activities besides the 3,8-divinyl chlorophyllide reductase activity, e.g. 7-hydroxymethyl chlorophyll a reductase activity. The Chl c2 to Chl c1 conversion is existent in cyanobacteria as a promiscuous activity of F-DVR. Chl c1 is synthesized by the reduction of the 8-vinyl group of Chl c2 or Chl c1 is synthesized from monovinyl-protochlorophyllide by the dehydrogenase
?
-
-
-
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.3.1.75
Arabidopsis thaliana
Q1H537
-
-
1.3.1.75
Phaeodactylum tricornutum
-
-
-
1.3.7.13
Synechocystis sp. PCC 6803
P74473
-
-
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.3.1.75
3,8-divinyl chlorophyll a + NADPH + H+
very low activity
746037
Phaeodactylum tricornutum
chlorophyll a + NADP+
-
-
-
?
1.3.1.75
3,8-divinyl chlorophyll a + NADPH + H+
very low activity
746037
Arabidopsis thaliana
chlorophyll a + NADP+
-
-
-
?
1.3.1.75
3,8-divinyl chlorophyllide a + NADPH + H+
-
746037
Phaeodactylum tricornutum
chlorophyllide a + NADP+
-
-
-
?
1.3.1.75
3,8-divinyl chlorophyllide a + NADPH + H+
-
746037
Arabidopsis thaliana
chlorophyllide a + NADP+
-
-
-
?
1.3.1.75
3,8-divinyl chlorophyllide a + NADPH + H+
low activity
746037
Arabidopsis thaliana
chlorophyllide a + NADP+
-
-
-
?
1.3.1.75
additional information
substrate specificity, overview. 3,8-Divinylprotochlorophyllide is a poor substrate, N-DVR has a high specificity for 3,8-divinyl chlorophyllide a
746037
Arabidopsis thaliana
?
-
-
-
-
1.3.1.75
additional information
substrate specificity, overview. Diatom N-DVR cannot convert 3,8-divinyl-protochlorophyllide a to 3-vinyl-protochlorophyllide a, but diatom N-DVR can efficiently utilize both 3,8-divinyl-chlorophyll a and 3,8-divinyl-chlorophyllide a, different from other N-DVRs, though in vitro, diatom N-DVR does not convert Chl c2 to Chl c1. No ferredoxin-dependent F-DVR activity, EC 1.3.7.13
746037
Phaeodactylum tricornutum
?
-
-
-
-
1.3.7.13
3,8-divinyl chlorophyll a + reduced ferredoxin [iron-sulfur] cluster + H+
-
746037
Synechocystis sp. PCC 6803
chlorophyll a + oxidized ferredoxin [iron-sulfur] cluster
-
-
-
?
1.3.7.13
3,8-divinyl chlorophyllide a + reduced ferredoxin [iron-sulfur] cluster + H+
-
746037
Synechocystis sp. PCC 6803
chlorophyllide a + oxidized ferredoxin [iron-sulfur] cluster
-
-
-
?
1.3.7.13
3,8-divinyl protochlorophyllide a + reduced ferredoxin [iron-sulfur] cluster + H+
-
746037
Synechocystis sp. PCC 6803
protochlorophyllide a + oxidized ferredoxin [iron-sulfur] cluster
-
-
-
?
1.3.7.13
additional information
cyanobacterial 3,8-divinyl chlorophyllide reductase (DVR) is a Chl biosynthetic enzyme that has many promiscuous activities besides the 3,8-divinyl chlorophyllide reductase activity, e.g. 7-hydroxymethyl chlorophyll a reductase activity. The Chl c2 to Chl c1 conversion is existent in cyanobacteria as a promiscuous activity of F-DVR. Chl c1 is synthesized by the reduction of the 8-vinyl group of Chl c2 or Chl c1 is synthesized from monovinyl-protochlorophyllide by the dehydrogenase
746037
Synechocystis sp. PCC 6803
?
-
-
-
-
1.3.7.13
additional information
substrate specificity, overview. Cyanobacterial F-DVR exhibits a broad substrate specificity and converts 3,8-divinylprotochlorophyllide a, 3,8-divinyl chlorophyllide a, and 3,8-divinyl chlorophyll a to the respective monovinyl molecules. When 7-hydroxymethyl chlorophyllide (HMChlide) a is incubated with F-DVR, chlorophyllide a is generated
746037
Synechocystis sp. PCC 6803
?
-
-
-
-
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.3.1.75
25
-
assay at
Arabidopsis thaliana
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.3.1.75
7.5
-
assay at
Arabidopsis thaliana
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.3.1.75
NADPH
dependent on
Arabidopsis thaliana
1.3.1.75
NADPH
dependent on
Phaeodactylum tricornutum
1.3.7.13
ferredoxin [iron-sulfur] cluster
dependent on
Synechocystis sp. PCC 6803
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
1.3.1.75
gene DVR, phylogenetic analysis
Arabidopsis thaliana
1.3.1.75
gene DVR, phylogenetic analysis, recombinant expression of NADPH-dependent DVR in Escherichia coli
Phaeodactylum tricornutum
1.3.7.13
gene slr1923, phylogenetic analysis
Synechocystis sp. PCC 6803
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.3.1.75
NADPH
dependent on
Arabidopsis thaliana
1.3.1.75
NADPH
dependent on
Phaeodactylum tricornutum
1.3.7.13
ferredoxin [iron-sulfur] cluster
dependent on
Synechocystis sp. PCC 6803
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.3.1.75
3,8-divinyl chlorophyll a + NADPH + H+
Phaeodactylum tricornutum
very low activity
chlorophyll a + NADP+
-
-
?
1.3.1.75
3,8-divinyl chlorophyllide a + NADPH + H+
Phaeodactylum tricornutum
-
chlorophyllide a + NADP+
-
-
?
1.3.1.75
3,8-divinyl chlorophyllide a + NADPH + H+
Arabidopsis thaliana
low activity
chlorophyllide a + NADP+
-
-
?
1.3.7.13
3,8-divinyl chlorophyll a + reduced ferredoxin [iron-sulfur] cluster + H+
Synechocystis sp. PCC 6803
-
chlorophyll a + oxidized ferredoxin [iron-sulfur] cluster
-
-
?
1.3.7.13
3,8-divinyl chlorophyllide a + reduced ferredoxin [iron-sulfur] cluster + H+
Synechocystis sp. PCC 6803
-
chlorophyllide a + oxidized ferredoxin [iron-sulfur] cluster
-
-
?
1.3.7.13
3,8-divinyl protochlorophyllide a + reduced ferredoxin [iron-sulfur] cluster + H+
Synechocystis sp. PCC 6803
-
protochlorophyllide a + oxidized ferredoxin [iron-sulfur] cluster
-
-
?
1.3.7.13
additional information
Synechocystis sp. PCC 6803
cyanobacterial 3,8-divinyl chlorophyllide reductase (DVR) is a Chl biosynthetic enzyme that has many promiscuous activities besides the 3,8-divinyl chlorophyllide reductase activity, e.g. 7-hydroxymethyl chlorophyll a reductase activity. The Chl c2 to Chl c1 conversion is existent in cyanobacteria as a promiscuous activity of F-DVR. Chl c1 is synthesized by the reduction of the 8-vinyl group of Chl c2 or Chl c1 is synthesized from monovinyl-protochlorophyllide by the dehydrogenase
?
-
-
-
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.3.1.75
3,8-divinyl chlorophyll a + NADPH + H+
very low activity
746037
Phaeodactylum tricornutum
chlorophyll a + NADP+
-
-
-
?
1.3.1.75
3,8-divinyl chlorophyll a + NADPH + H+
very low activity
746037
Arabidopsis thaliana
chlorophyll a + NADP+
-
-
-
?
1.3.1.75
3,8-divinyl chlorophyllide a + NADPH + H+
-
746037
Phaeodactylum tricornutum
chlorophyllide a + NADP+
-
-
-
?
1.3.1.75
3,8-divinyl chlorophyllide a + NADPH + H+
-
746037
Arabidopsis thaliana
chlorophyllide a + NADP+
-
-
-
?
1.3.1.75
3,8-divinyl chlorophyllide a + NADPH + H+
low activity
746037
Arabidopsis thaliana
chlorophyllide a + NADP+
-
-
-
?
1.3.1.75
additional information
substrate specificity, overview. 3,8-Divinylprotochlorophyllide is a poor substrate, N-DVR has a high specificity for 3,8-divinyl chlorophyllide a
746037
Arabidopsis thaliana
?
-
-
-
-
1.3.1.75
additional information
substrate specificity, overview. Diatom N-DVR cannot convert 3,8-divinyl-protochlorophyllide a to 3-vinyl-protochlorophyllide a, but diatom N-DVR can efficiently utilize both 3,8-divinyl-chlorophyll a and 3,8-divinyl-chlorophyllide a, different from other N-DVRs, though in vitro, diatom N-DVR does not convert Chl c2 to Chl c1. No ferredoxin-dependent F-DVR activity, EC 1.3.7.13
746037
Phaeodactylum tricornutum
?
-
-
-
-
1.3.7.13
3,8-divinyl chlorophyll a + reduced ferredoxin [iron-sulfur] cluster + H+
-
746037
Synechocystis sp. PCC 6803
chlorophyll a + oxidized ferredoxin [iron-sulfur] cluster
-
-
-
?
1.3.7.13
3,8-divinyl chlorophyllide a + reduced ferredoxin [iron-sulfur] cluster + H+
-
746037
Synechocystis sp. PCC 6803
chlorophyllide a + oxidized ferredoxin [iron-sulfur] cluster
-
-
-
?
1.3.7.13
3,8-divinyl protochlorophyllide a + reduced ferredoxin [iron-sulfur] cluster + H+
-
746037
Synechocystis sp. PCC 6803
protochlorophyllide a + oxidized ferredoxin [iron-sulfur] cluster
-
-
-
?
1.3.7.13
additional information
cyanobacterial 3,8-divinyl chlorophyllide reductase (DVR) is a Chl biosynthetic enzyme that has many promiscuous activities besides the 3,8-divinyl chlorophyllide reductase activity, e.g. 7-hydroxymethyl chlorophyll a reductase activity. The Chl c2 to Chl c1 conversion is existent in cyanobacteria as a promiscuous activity of F-DVR. Chl c1 is synthesized by the reduction of the 8-vinyl group of Chl c2 or Chl c1 is synthesized from monovinyl-protochlorophyllide by the dehydrogenase
746037
Synechocystis sp. PCC 6803
?
-
-
-
-
1.3.7.13
additional information
substrate specificity, overview. Cyanobacterial F-DVR exhibits a broad substrate specificity and converts 3,8-divinylprotochlorophyllide a, 3,8-divinyl chlorophyllide a, and 3,8-divinyl chlorophyll a to the respective monovinyl molecules. When 7-hydroxymethyl chlorophyllide (HMChlide) a is incubated with F-DVR, chlorophyllide a is generated
746037
Synechocystis sp. PCC 6803
?
-
-
-
-
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.3.1.75
25
-
assay at
Arabidopsis thaliana
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.3.1.75
7.5
-
assay at
Arabidopsis thaliana
General Information
EC Number
General Information
Commentary
Organism
1.3.1.75
evolution
either F-DVR or N-DVR is found in most photosynthetic organisms, yet both F-DVR and N-DVR exist in the genome of diatoms that contain Chl a and Chl c1
Arabidopsis thaliana
1.3.1.75
evolution
either F-DVR or N-DVR is found in most photosynthetic organisms, yet both F-DVR and N-DVR exist in the genome of diatoms that contain Chl a and Chl c1. Diatom N-DVR has evolved to function in Chl a biosynthesis, and diatom F-DVR is responsible for the biosynthesis of Chl c1 from Chl c2
Phaeodactylum tricornutum
1.3.1.75
metabolism
the enzyme is involved the chlorophyll biosynthetic pathways of oxygenic photosynthetic organisms. At the later steps of chlorophyll biosynthesis, 3,8-divinyl-chlorophyllide (Chlide) a is converted to monovinyl (MV)-Chlide a by DVR
Arabidopsis thaliana
1.3.1.75
metabolism
the enzyme is involved the chlorophyll biosynthetic pathways of oxygenic photosynthetic organisms. At the later steps of chlorophyll biosynthesis, 3,8-divinyl-chlorophyllide (Chlide) a is converted to monovinyl (MV)-Chlide a by DVR
Phaeodactylum tricornutum
1.3.7.13
evolution
either F-DVR or N-DVR is found in most photosynthetic organisms, yet both F-DVR and N-DVR exist in the genome of diatoms that contain Chl a and Chl c1
Synechocystis sp. PCC 6803
1.3.7.13
metabolism
the enzyme is involved the chlorophyll biosynthetic pathways of oxygenic photosynthetic organisms. At the later steps of chlorophyll biosynthesis, 3,8-divinyl-chlorophyllide (Chlide) a is converted to monovinyl (MV)-Chlide a by DVR. Involvement of DVR in Chl c biosynthesis
Synechocystis sp. PCC 6803
General Information (protein specific)
EC Number
General Information
Commentary
Organism
1.3.1.75
evolution
either F-DVR or N-DVR is found in most photosynthetic organisms, yet both F-DVR and N-DVR exist in the genome of diatoms that contain Chl a and Chl c1
Arabidopsis thaliana
1.3.1.75
evolution
either F-DVR or N-DVR is found in most photosynthetic organisms, yet both F-DVR and N-DVR exist in the genome of diatoms that contain Chl a and Chl c1. Diatom N-DVR has evolved to function in Chl a biosynthesis, and diatom F-DVR is responsible for the biosynthesis of Chl c1 from Chl c2
Phaeodactylum tricornutum
1.3.1.75
metabolism
the enzyme is involved the chlorophyll biosynthetic pathways of oxygenic photosynthetic organisms. At the later steps of chlorophyll biosynthesis, 3,8-divinyl-chlorophyllide (Chlide) a is converted to monovinyl (MV)-Chlide a by DVR
Arabidopsis thaliana
1.3.1.75
metabolism
the enzyme is involved the chlorophyll biosynthetic pathways of oxygenic photosynthetic organisms. At the later steps of chlorophyll biosynthesis, 3,8-divinyl-chlorophyllide (Chlide) a is converted to monovinyl (MV)-Chlide a by DVR
Phaeodactylum tricornutum
1.3.7.13
evolution
either F-DVR or N-DVR is found in most photosynthetic organisms, yet both F-DVR and N-DVR exist in the genome of diatoms that contain Chl a and Chl c1
Synechocystis sp. PCC 6803
1.3.7.13
metabolism
the enzyme is involved the chlorophyll biosynthetic pathways of oxygenic photosynthetic organisms. At the later steps of chlorophyll biosynthesis, 3,8-divinyl-chlorophyllide (Chlide) a is converted to monovinyl (MV)-Chlide a by DVR. Involvement of DVR in Chl c biosynthesis
Synechocystis sp. PCC 6803