BRENDA - Enzyme Database show
show all sequences of 1.3.7.7

X-ray crystal structure of the light-independent protochlorophyllide reductase

Muraki, N.; Nomata, J.; Ebata, K.; Mizoguchi, T.; Shiba, T.; Tamiaki, H.; Kurisu, G.; Fujita, Y.; Nature 465, 110-114 (2010)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
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
Rhodobacter capsulatus
Crystallization (Commentary)
Crystallization
Organism
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
Rhodobacter capsulatus
Engineering
Amino acid exchange
Commentary
Organism
C112A
inactive
Rhodobacter capsulatus
C26A
inactive
Rhodobacter capsulatus
C51A
the mutation almost abolishes the activity of the enzyme (less than 5% compared to the wild type enzyme)
Rhodobacter capsulatus
C95A
inactive
Rhodobacter capsulatus
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)
Rhodobacter capsulatus
D36C
site-directed mutagenesis, mutation in BchB, mutant NB-cluster structure compered to the wild-type enzyme; the mutation almost abolishes the activity of the enzyme (less than 5% compared to the wild type enzyme)
Rhodobacter capsulatus
D36S
site-directed mutagenesis, mutation in BchB, mutant NB-cluster structure compered to the wild-type enzyme; the mutation almost abolishes the activity of the enzyme (less than 5% compared to the wild type enzyme)
Rhodobacter capsulatus
Inhibitors
Inhibitors
Commentary
Organism
Structure
chlorophyll c
competitive inhibitor
Rhodobacter capsulatus
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
iron-sulfur cluster in the NB protein
Rhodobacter capsulatus
Mg2+
-
Rhodobacter capsulatus
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
chlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
Rhodobacter capsulatus
-
protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate + 2 H+
-
-
?
chlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
Rhodobacter capsulatus DB176
-
protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate + 2 H+
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Rhodobacter capsulatus
-
-
-
Rhodobacter capsulatus DB176
-
-
-
Purification (Commentary)
Commentary
Organism
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
Rhodobacter capsulatus
Reaction
Reaction
Commentary
Organism
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate = protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
reaction mechanism for trans-specific reduction, overview
Rhodobacter capsulatus
Specific Activity [micromol/min/mg]
Specific Activity Minimum [µmol/min/mg]
Specific Activity Maximum [µmol/min/mg]
Commentary
Organism
0.026
-
purified recombinant protochlorophyllide-bound NB-protein, recovered from crystals, pH not specified in the publication, temperature not specified in the publication
Rhodobacter capsulatus
0.05
-
purified recombinant protochlorophyllide-free NB-protein, recovered from crystals, pH not specified in the publication, temperature not specified in the publication
Rhodobacter capsulatus
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
chlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
-
713102
Rhodobacter capsulatus
protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate + 2 H+
-
-
-
?
chlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
-
713102
Rhodobacter capsulatus DB176
protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate + 2 H+
-
-
-
?
chlorophyllide a + reduced ferredoxin + ATP
-
713102
Rhodobacter capsulatus
protochlorophyllide + oxidized ferredoxin + ADP + phosphate
-
-
-
?
chlorophyllide a + reduced ferredoxin + ATP
-
713102
Rhodobacter capsulatus DB176
protochlorophyllide + oxidized ferredoxin + ADP + phosphate
-
-
-
?
additional information
DPOR is a nitrogenase-like enzyme consisting of two components, L-protein (a BchL dimer) and NB-protein (a BchN-BchB heterotetramer)
713102
Rhodobacter capsulatus
?
-
-
-
-
additional information
each catalytic BchN-BchB unit contains one protochlorophyllidee and one iron-sulfur NB-cluster coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific protochlorophyllide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit, unique trans-specific reduction mechanism in which the distorted C17-propionate of protochlorophyllid and an aspartate from BchB serve as proton donors for C18 and C17 of protochlorophyllide, respectively, overview
713102
Rhodobacter capsulatus
?
-
-
-
-
additional information
the C175C18 double bond of chlorophyll c is not reduced by DPOR
713102
Rhodobacter capsulatus
?
-
-
-
-
additional information
DPOR is a nitrogenase-like enzyme consisting of two components, L-protein (a BchL dimer) and NB-protein (a BchN-BchB heterotetramer)
713102
Rhodobacter capsulatus DB176
?
-
-
-
-
additional information
each catalytic BchN-BchB unit contains one protochlorophyllidee and one iron-sulfur NB-cluster coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific protochlorophyllide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit, unique trans-specific reduction mechanism in which the distorted C17-propionate of protochlorophyllid and an aspartate from BchB serve as proton donors for C18 and C17 of protochlorophyllide, respectively, overview
713102
Rhodobacter capsulatus DB176
?
-
-
-
-
additional information
the C175C18 double bond of chlorophyll c is not reduced by DPOR
713102
Rhodobacter capsulatus DB176
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
heterooctamer
(alpha2)2(betagamma)4, DPOR is a nitrogenase-like enzyme consisting of two components, L-protein, a BchL dimer, and NB-protein, a BchN-BchB heterotetramer, which are structurally related to nitrogenase Fe protein and MoFe protein, respectively
Rhodobacter capsulatus
More
each catalytic BchN-BchB unit contains one protochlorophyllide and one iron-sulfur NB-cluster coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific protochlorophyllide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit, unique trans-specific reduction mechanism in which the distorted C17-propionate of protochlorophyllide and an aspartate from BchB serve as proton donors for C18 and C17 of protochlorophyllide, respectively, overview
Rhodobacter capsulatus
Cofactor
Cofactor
Commentary
Organism
Structure
4Fe-4S-center
-
Rhodobacter capsulatus
ATP
-
Rhodobacter capsulatus
Ferredoxin
each catalytic BchN-BchB unit contains one protochlorophyllidee and one iron-sulfur NB-cluster coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity, overview
Rhodobacter capsulatus
Cloned(Commentary) (protein specific)
Commentary
Organism
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
Rhodobacter capsulatus
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
4Fe-4S-center
-
Rhodobacter capsulatus
ATP
-
Rhodobacter capsulatus
Ferredoxin
each catalytic BchN-BchB unit contains one protochlorophyllidee and one iron-sulfur NB-cluster coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity, overview
Rhodobacter capsulatus
Crystallization (Commentary) (protein specific)
Crystallization
Organism
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
Rhodobacter capsulatus
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
C112A
inactive
Rhodobacter capsulatus
C26A
inactive
Rhodobacter capsulatus
C51A
the mutation almost abolishes the activity of the enzyme (less than 5% compared to the wild type enzyme)
Rhodobacter capsulatus
C95A
inactive
Rhodobacter capsulatus
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)
Rhodobacter capsulatus
D36C
site-directed mutagenesis, mutation in BchB, mutant NB-cluster structure compered to the wild-type enzyme; the mutation almost abolishes the activity of the enzyme (less than 5% compared to the wild type enzyme)
Rhodobacter capsulatus
D36S
site-directed mutagenesis, mutation in BchB, mutant NB-cluster structure compered to the wild-type enzyme; the mutation almost abolishes the activity of the enzyme (less than 5% compared to the wild type enzyme)
Rhodobacter capsulatus
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
chlorophyll c
competitive inhibitor
Rhodobacter capsulatus
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
iron-sulfur cluster in the NB protein
Rhodobacter capsulatus
Mg2+
-
Rhodobacter capsulatus
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
chlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
Rhodobacter capsulatus
-
protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate + 2 H+
-
-
?
chlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
Rhodobacter capsulatus DB176
-
protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate + 2 H+
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
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
Rhodobacter capsulatus
Specific Activity [micromol/min/mg] (protein specific)
Specific Activity Minimum [µmol/min/mg]
Specific Activity Maximum [µmol/min/mg]
Commentary
Organism
0.026
-
purified recombinant protochlorophyllide-bound NB-protein, recovered from crystals, pH not specified in the publication, temperature not specified in the publication
Rhodobacter capsulatus
0.05
-
purified recombinant protochlorophyllide-free NB-protein, recovered from crystals, pH not specified in the publication, temperature not specified in the publication
Rhodobacter capsulatus
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
chlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
-
713102
Rhodobacter capsulatus
protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate + 2 H+
-
-
-
?
chlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
-
713102
Rhodobacter capsulatus DB176
protochlorophyllide + oxidized ferredoxin + 2 ADP + 2 phosphate + 2 H+
-
-
-
?
chlorophyllide a + reduced ferredoxin + ATP
-
713102
Rhodobacter capsulatus
protochlorophyllide + oxidized ferredoxin + ADP + phosphate
-
-
-
?
chlorophyllide a + reduced ferredoxin + ATP
-
713102
Rhodobacter capsulatus DB176
protochlorophyllide + oxidized ferredoxin + ADP + phosphate
-
-
-
?
additional information
DPOR is a nitrogenase-like enzyme consisting of two components, L-protein (a BchL dimer) and NB-protein (a BchN-BchB heterotetramer)
713102
Rhodobacter capsulatus
?
-
-
-
-
additional information
each catalytic BchN-BchB unit contains one protochlorophyllidee and one iron-sulfur NB-cluster coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific protochlorophyllide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit, unique trans-specific reduction mechanism in which the distorted C17-propionate of protochlorophyllid and an aspartate from BchB serve as proton donors for C18 and C17 of protochlorophyllide, respectively, overview
713102
Rhodobacter capsulatus
?
-
-
-
-
additional information
the C175C18 double bond of chlorophyll c is not reduced by DPOR
713102
Rhodobacter capsulatus
?
-
-
-
-
additional information
DPOR is a nitrogenase-like enzyme consisting of two components, L-protein (a BchL dimer) and NB-protein (a BchN-BchB heterotetramer)
713102
Rhodobacter capsulatus DB176
?
-
-
-
-
additional information
each catalytic BchN-BchB unit contains one protochlorophyllidee and one iron-sulfur NB-cluster coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific protochlorophyllide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit, unique trans-specific reduction mechanism in which the distorted C17-propionate of protochlorophyllid and an aspartate from BchB serve as proton donors for C18 and C17 of protochlorophyllide, respectively, overview
713102
Rhodobacter capsulatus DB176
?
-
-
-
-
additional information
the C175C18 double bond of chlorophyll c is not reduced by DPOR
713102
Rhodobacter capsulatus DB176
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
heterooctamer
(alpha2)2(betagamma)4, DPOR is a nitrogenase-like enzyme consisting of two components, L-protein, a BchL dimer, and NB-protein, a BchN-BchB heterotetramer, which are structurally related to nitrogenase Fe protein and MoFe protein, respectively
Rhodobacter capsulatus
More
each catalytic BchN-BchB unit contains one protochlorophyllide and one iron-sulfur NB-cluster coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific protochlorophyllide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit, unique trans-specific reduction mechanism in which the distorted C17-propionate of protochlorophyllide and an aspartate from BchB serve as proton donors for C18 and C17 of protochlorophyllide, respectively, overview
Rhodobacter capsulatus
General Information
General Information
Commentary
Organism
physiological function
DPOR performs reduction of the C17-C18 double bond of protochlorophyllide to form chlorophyllide a, the direct precursor of chlorophyll a in a light-independent, dark-operative way of action
Rhodobacter capsulatus
General Information (protein specific)
General Information
Commentary
Organism
physiological function
DPOR performs reduction of the C17-C18 double bond of protochlorophyllide to form chlorophyllide a, the direct precursor of chlorophyll a in a light-independent, dark-operative way of action
Rhodobacter capsulatus
Other publictions for EC 1.3.7.7
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
743315
Zhang
The SWI2/SNF2 chromatin-remod ...
Arabidopsis thaliana
Mol. Plant
10
155-167
2017
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1
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1
1
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741827
Nomata
Stoichiometry of ATP hydrolys ...
Rhodobacter capsulatus, Rhodobacter capsulatus ATCC BAA-309
Biochem. Biophys. Res. Commun.
470
704-709
2016
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743401
Silva
With or without light compari ...
Rhodobacter capsulatus, Rhodobacter capsulatus ATCC BAA-309
PeerJ
2
e551
2014
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726255
Kopecna
Inhibition of chlorophyll bios ...
Synechocystis sp.
Planta
237
497-508
2013
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1
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1
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2
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726394
Moser
Structure of ADP-aluminium flu ...
Prochlorococcus marinus
Proc. Natl. Acad. Sci. USA
110
2094-2098
2013
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1
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2
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6
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1
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3
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725926
Nazir
Chloroplast-encoded chlB gene ...
Pinus thunbergii
Mol. Biol. Rep.
39
10637-10646
2012
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1
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1
1
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712026
Kondo
EPR study of 1Asp-3Cys ligated ...
Rhodobacter capsulatus
FEBS Lett.
585
214-218
2011
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1
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725877
Moser
Methods for nitrogenase-like d ...
Prochlorococcus marinus
Methods Mol. Biol.
766
129-143
2011
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