Information on EC 1.3.7.7 - ferredoxin:protochlorophyllide reductase (ATP-dependent)

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
1.3.7.7
-
RECOMMENDED NAME
GeneOntology No.
ferredoxin:protochlorophyllide reductase (ATP-dependent)
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate = protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)
-
-
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)
-
-
Biosynthesis of secondary metabolites
-
-
Metabolic pathways
-
-
Porphyrin and chlorophyll metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP-dependent ferredoxin:protochlorophyllide-a 7,8-oxidoreductase
Occurs in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms. The enzyme catalyses trans-reduction of the D-ring of protochlorophyllide; the product has the (7S,8S)-configuration. Unlike EC 1.3.1.33 (protochlorophyllide reductase), light is not required. The enzyme contains a [4Fe-4S] cluster, and structurally resembles the Fe protein/MoFe protein complex of nitrogenase (EC 1.18.6.1), which catalyses an ATP-driven reduction.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
subunit B, subunit L, and subunit N; strain CS-41, also named Auxenochlorella protothecoides strain CS-41
Q6VQA8 and Q6VQA9 and Q7YKW4
UniProt
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L631 and Q2L630 and Q2L629
UniProt
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L634 and Q2L633 and Q2L632
UniProt
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L637 and Q2L636 and Q2L635
UniProt
Manually annotated by BRENDA team
three subunits of DPOR, encoded by genes bchL, bchN and bchB
-
-
Manually annotated by BRENDA team
three subunits of DPOR, encoded by genes bchL, bchN and bchB
-
-
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L646 and Q2L645 and Q2L644
UniProt
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L604 and Q2L603 and Q2L602
UniProt
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L628 and Q2L627 and Q2L626
UniProt
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L643 and Q2L642 and Q2L641
UniProt
Manually annotated by BRENDA team
three subunits of DPOR, encoded by genes bchL, bchN and bchB
-
-
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N; variant Juniperus chinensis procumbens
Q2L622 and Q2L621 and Q2L620
UniProt
Manually annotated by BRENDA team
subunit B, subunit L and subunit N
Q2L625 and Q2L624 and Q2L623
UniProt
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L658 and Q2L657 and Q2L656
UniProt
Manually annotated by BRENDA team
no activity in Hordeum vulgare
-
-
-
Manually annotated by BRENDA team
no activity in Thuja occidentalis
-
-
-
Manually annotated by BRENDA team
no activity in Thuja plicata
-
-
-
Manually annotated by BRENDA team
no activity in Thuja standishii
-
-
-
Manually annotated by BRENDA team
gene chlB; three constitutive plastid genes chlL, chlN, and chlB
UniProt
Manually annotated by BRENDA team
gene chlB; three constitutive plastid genes chlL, chlN, and chlB
UniProt
Manually annotated by BRENDA team
loblolly pine
-
-
Manually annotated by BRENDA team
gene chlB encoding the ChlB subunit of the enzyme complex
-
-
Manually annotated by BRENDA team
subunit B, subunit L and subunit N
Q2L619 and Q2L618 and Q2L617
UniProt
Manually annotated by BRENDA team
subunit bchL; strain SB1003
UniProt
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L655 and Q2L654 and Q2L653
UniProt
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L652 and Q2L651 and Q2L650
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
subunit B, subunit L, and subunit N
Q2L640 and Q2L639 and Q2L638
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
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a strain lacking DPOR contains about 25% of the wild-type level of photosystems PSII and PSI when cultivated under light-activated heterotrophic growth conditions. Deletion of the chlL gene abolishes activity of the DPOR enzyme. Absence of the chlL gene causes a further 20% decrease in Chl content and therefore the resulting (pCER:por)/Dpor/DchlL strain termed SynPORreg reaches only 60-70% of Chl content present in wild-type
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
chlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate + 2 H+
show the reaction diagram
chlorophyllide a + reduced ferredoxin + ATP
protochlorophyllide + oxidized ferredoxin + ADP + phosphate
show the reaction diagram
protochlorophyllide + oxidized ferredoxin + ADP + phosphate
chlorophyllide a + reduced ferredoxin + ATP
show the reaction diagram
protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
chlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate + 2 H+
show the reaction diagram
chlorophyllide a + reduced ferredoxin + ATP
protochlorophyllide + oxidized ferredoxin + ADP + phosphate
show the reaction diagram
Q6VQA8 and Q6VQA9 and Q7YKW4
-
-
-
?
protochlorophyllide + oxidized ferredoxin + ADP + phosphate
chlorophyllide a + reduced ferredoxin + ATP
show the reaction diagram
protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate
show the reaction diagram
additional information
?
-
-
proposed catalytic redox cycle of DPOR, overview
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-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4Fe-4S-center
Ferredoxin
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
chlorophyll c
-
competitive inhibitor
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Dithionite
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dark protochlorophyllide reductase activity is dependent on the reductant dithionite
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0106
protochlorophyllide
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in 100 mM HEPES-KOH (pH 7.4), 5 mM MgCl2, 5 mM dithiothreitol, at 34°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.026
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purified recombinant protochlorophyllide-bound NB-protein, recovered from crystals, pH not specified in the publication, temperature not specified in the publication
0.0262
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purified enzyme, pH not specified in the publication, at 34°C
0.05
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purified recombinant protochlorophyllide-free NB-protein, recovered from crystals, pH not specified in the publication, temperature not specified in the publication
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
cotyldedons of darkgrown seedlings
Manually annotated by BRENDA team
-
stems of darkgrown seedlings
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
cytoplasmic or thylakoid membranes
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
31000
-
2 * 31000, L-protein of DPOR, SDS-PAGE
33310
calculated from amino acid sequence
33380
mass spectroscopy
33413
-
2 * 33413, L-protein of DPOR, calculated from amino acid sequence
35000
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octameric (ChlN/ChlB)2(ChlL2)2 subunit complex, 4 * 35000, subunit ChlL, + 2 * 45000, subunit ChlN, 2 * 60000, subunit ChlB, SDS-PAGE, 4 * 32395,subunit ChlL, + 2 * 46199, subunit ChlN, 2 * 58729, subunit ChlB, sequence calculation
36000
-
2 * 36000, S-tag subunit BchL, SDS-PAGE
36046
-
2 * 36046, subunit BchL calculated from amino acid sequence
38000
Q6VQA8 and Q6VQA9 and Q7YKW4
1 * 38000 + 1 * 49000 + 1 * 58000, SDS-PAGE
43000
-
2 * 51000 + 2 * 43000 , NB-protein of DPOR, SDS-PAGE
45000
-
octameric (ChlN/ChlB)2(ChlL2)2 subunit complex, 4 * 35000, subunit ChlL, + 2 * 45000, subunit ChlN, 2 * 60000, subunit ChlB, SDS-PAGE, 4 * 32395,subunit ChlL, + 2 * 46199, subunit ChlN, 2 * 58729, subunit ChlB, sequence calculation
46038
-
2 * 57191 + 2 * 46038, NB-protein of DPOR, calculated from amino acid sequence
46199
-
octameric (ChlN/ChlB)2(ChlL2)2 subunit complex, 4 * 35000, subunit ChlL, + 2 * 45000, subunit ChlN, 2 * 60000, subunit ChlB, SDS-PAGE, 4 * 32395,subunit ChlL, + 2 * 46199, subunit ChlN, 2 * 58729, subunit ChlB, sequence calculation
48671
-
2 * 48671 + 2 * 57191, subunit BchN and subunit BchB, calculated from amino acid sequence
49000
Q6VQA8 and Q6VQA9 and Q7YKW4
1 * 38000 + 1 * 49000 + 1 * 58000, SDS-PAGE
51000
-
2 * 51000 + 2 * 43000 , NB-protein of DPOR, SDS-PAGE
52000
-
2 * 52000 + 2 * 60000, NB-protein complex, SDS-PAGE
56820
-
subunit ChlB, calculated from amino acid sequence
58729
-
octameric (ChlN/ChlB)2(ChlL2)2 subunit complex, 4 * 35000, subunit ChlL, + 2 * 45000, subunit ChlN, 2 * 60000, subunit ChlB, SDS-PAGE, 4 * 32395,subunit ChlL, + 2 * 46199, subunit ChlN, 2 * 58729, subunit ChlB, sequence calculation
67000
-
S-tag subunit BchL, gel filtration
200000
-
NB-protein complex, gel filtration
360000
-
enzyme complex, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterodimer
Q6VQA8 and Q6VQA9 and Q7YKW4
1 * 38000 + 1 * 49000 + 1 * 58000, SDS-PAGE
heterooctamer
heterotetramer
homodimer
octamer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
substrate-bound, ADP-aluminium fluoride-stabilized transition state complex between the DPOR components L2 and (NB)2, sitting drops by vapor diffusion, mixing of 0.001 ml of protein solution containing 7.5 mg/ml protein in 100 mM HEPES/NaOH, pH 7.5, 150 mM NaCl, 10 mM MgCl2, 50 mM NaF, and 2 mM AlCl3,with 0.001 ml of reservoir solution containing 0.1 M KCl, 0.1 M Tris, pH 8.5, and 3% wt/v PEG 6000, 17°C, X-ray diffraction structure determination and analysis at 2.1 A resolution
catalytic component NB-protein, both in thePchlide-bound and Pchlide-free states, X-ray diffraction structure determination at 2.3 A and 2.8 A resolution, respectively
-
hanging drop vapor diffusion method, the protochlorophyllide-bound form of NB-protein is crystallized using 200 mM sodium/potassium phosphate buffer (pH 5.0) containing 5 mM dithiothreitol and 10% (w/v) ethylene glycol at 4°C, to which 16% (w/v) and 14% (w/v) PEG4K are added in aerobic and anaerobic conditions, respectively, as precipitants. Protochlorophyllide -free and selenomethionine-substituted recombinant NB-proteins are crystallized at 20°C using 20% (w/v) PEG3350 containing 200 mM ammonium chloride and 5mM dithiothreitol. D36C and D36A variants are crystallized at 4°C using 20% (w/v) PEG3350 containing 200 mM sodium chloride, 100 mM MOPS/NaOH (pH 7.0) and 5 mM dithiothreitol as a precipitant; purified recombinant protochlorophyllide-bound and protochlorophyllide-free forms of NB-protein of DPOR, and purified recombinant selenomethionine-substituted protochlorophyllide-free forms of mutants D36A and D36C, hanging-drop vapour diffusion method., X-ray diffraction structure determination and analysis at 2.3-2.9 A resolution
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L-protein in the MgADP-bound form, X-ray diffraction structure determination at 1.6 A resolution
-
L-protein of DPOR with Mg-ADP bound, microcapillary batch diffusion method, with 20-25% (w/v) PEG 3350 as the precipitating agent, with 200 mM magnesium formate (pH 7.7)
native and SeMet-labeled catalytic (ChlN/ChlB)2 complex, hanging drop vapor diffusion, 17°C, mixing of 0.003 ml of 10 mg/ml protein in 100 mM HEPES-NaOH, pH 7.5, 150 mM NaCl, and 10 mM MgCl2, with 0.003 ml of reservoir solution consisting of 9.5% PEG 6000, 85 mM HEPES-NaOH, pH 7.1, 14.3% 2-methyl pentane-2,4-diol, and 15% glycerol as cryoprotectants or 10.5% PEG 6000, 85 mM HEPES-NaOH, pH7.5, 14.3% 2-methyl pentane-2,4-diol, and 15% glycerol as cryoprotectants for selenomethionine-labeled protein, 3-5 days,X-ray diffraction structure determination and analysis at 2.4-2.81 A resolution
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
the NB-protein activity persists after the exposure to air for almost 2 h
-
686758
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, NB- and L-protein subunits of the crude extract when maintained anaerobically, more than 6 months, remain stable with no significant loss of activity
-
4°C, NB- and L-protein subunits of the purified extract when maintained anaerobically, both activities of the components are rapidly lost during purification procedures such as affinity chromatography with S-protein agarose
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
HiTrap chelating column chromatography and Superdex 200pg gel filtration
-
protochlorophyllide-saturated NB-protein from DPOR is purified by Strep-Tactin Sepharose column chromatography
-
purification by immobilization of GST-tagged subunit L2 on glutathione resin, complex formation with purified subunits NB, and proteolytical cleavage
recombinant N-terminally GST-tagged (ChlN/ChlB)2 complex by glutathione affinity chromatography, and gel filtration and ultrafiltration
-
recombinant protochlorophyllide-bound and protochlorophyllide-free forms of NB-protein from Rhodobacter capsulatus strain DB176 and Escherichia coli strain JM105 by affinity chromatography and gel filtration; Strep-tactin column chromatography and Superdex 200 gel filtration
-
S protein-agarose column chromatography
-
S-protein agarose column chromatography
-
zinc-loaded chelating Sepharose column chromatography and Q-Sepharose column chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination, analysis, and comparison
expressed in Azotobacter vinelandii strain DJ884
expressed in Escherichia coli BL21(DE3)Lys cells
Q6VQA8 and Q6VQA9 and Q7YKW4
expressed in Escherichia coli JM105 cells; protochlorophyllide-bound and protochlorophyllide-free forms of NB-protein are overexpressed in Rhodobacter capsulatus strain DB176 and Escherichia coli strain JM105
-
expressed in Rhodobacter capsulatus mutant DB176 cells
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expression of N-terminally GST-tagged (ChlN/ChlB)2 complex
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gene chlB, DNA and amino acid sequence determination, analysis, and comparison
gene chlB, stable integration of the chlB gene from Pinus thunbergii into the chloroplast genome of tobacco, the ChlB subunit in transgenic Nicotana tabacum var. Petit Havana causes a early development of chlorophyll pigments in leaves of the transgenic shoots compared to the wild type shoots and altered root development. The chlB gene is involved, directly or indirectly, in the root development of tobacco, phenotype, overviews
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His-tagged subunit ChlB fusion protein is expressed in Escherichia coli JM105 cells
-
subunits BchL and BchN are expressed in Rhodobacter capsulatus strains YCN1 or YCL3 as S tag fusion proteins, subunit BchB is co-purified with the BchN protein
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
DPOR gene transcripts are down-regulated 2-5fold in the dark; DPOR gene transcripts are down-regulated 2-5fold in the dark. After a brief increase at 30 min the transcript level of DPOR subunit N drops precipitously, and within 4 h in the dark the DPOR subunit N transcript levels are just under 20% of those of green light-grown cells; DPOR gene transcripts are down-regulated 2-5fold in the dark. Within 30 min in the dark the DPOR subunit B transcript abundance drops to approximately 70% that of green light-grown cells and remains at that level before dropping to approximately 40% that of green light-grown cells at 4 h
the highest levels of the three plastid gene transcripts chlL, chlN, and chlB encoding subunits of the light-independent protochlorophyllide reductase are detected within the top one-third of the stem and decrease gradually towards the stem/root transition zone in dark-grown seedlings
-
the level of theLIPOR subunit L mRNA of Chlorella protothecoides strain CS-41 is much higher in the light than in the dark
Q6VQA8 and Q6VQA9 and Q7YKW4
the transcript level of DPOR subunit B is up-regulated approximately 2fold in green light relative to levels in red light; transcripts levels of all DPOR genes are up-regulated approximately 2fold in green light relative to levels in red light; transcripts levels of all DPOR genes are up-regulated approximately 2fold in green light relative to levels in red light
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C112A
-
inactive
C26A
-
inactive
C51A
-
the mutation almost abolishes the activity of the enzyme (less than 5% compared to the wild type enzyme)
C95A
-
inactive
C112A
-
inactive
-
C26A
-
inactive
-
C51A
-
the mutation almost abolishes the activity of the enzyme (less than 5% compared to the wild type enzyme)
-
D36A
-
site-directed mutagenesis, mutation in BchB, mutant NB-cluster structure compered to the wild-type enzyme; the mutant exhibits low activity (13% compared to the wild type enzyme)
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C95A
-
inactive protein, probably due to destabilization of the [4Fe-4S] cluster environment
C95S
-
inactive protein, probably due to destabilization of the [4Fe-4S] cluster environment
additional information
Show AA Sequence (2948 entries)
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