BRENDA - Enzyme Database show
show all sequences of 1.3.7.12

Crystal structures of the substrate-bound forms of red chlorophyll catabolite reductase: implications for site-specific and stereospecific reaction

Sugishima, M.; Okamoto, Y.; Noguchi, M.; Kohchi, T.; Tamiaki, H.; Fukuyama, K.; J. Mol. Biol. 402, 879-891 (2010)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression of GST-tagged wild-type and F218V mutant RCCR lacking the chloroplast transit peptide, Met1 to Gln39; expression of wild-type and mutant enzymes lacking the chloroplast transit peptide (Met1 to Gln39) and N-termial residues 40-48 as GST-tagged enzymes
Arabidopsis thaliana
Crystallization (Commentary)
Crystallization
Organism
purified recombinant RCC-bound wild-type enzyme AtRCCRDELTA49, RCC-bound and substrate-free enzyme mutant F218V AtRCCRDELTA49, sitting-drop vapor diffusion method, mixing of 10 mg/ml substrate-free and substrate-bound proteins in 20 mM Tris-HCl, pH 7.4, and 200 mM NaCl, with an equal volume of reservoir solution containing 30% or 35%, respectively, w/v PEG 2000 monomethyl ether, 0.1 M ammonium acetate, 3% v/v dioxane, and 0.1 M 4-morpholineethanesulfonic acid-NaOH, pH 6.5, equilibration gainst reservoir solution, 20°C, 1 day, X-ray diffraction structure determination and analysis at 2.0-2.6 A resolution; purified recombinant red chlorophyll catabolite-bound RCCRDELTA49, and red chlorophyll catabolite-bound or substrate-free F218V RCCRDELTA49, sitting drop vapor diffusion method, 20°C, protein solution is mixed with an equal volume of reservoir solution and equilibrated against reservoir solution containing 30% w/v PEG 2000 monomethyl ether, 0.1 M ammonium acetate, 3% v/v dioxane, and 0.1 M 4-morpholineethanesulfonic acid-NaOH, pH 6.5, 1 day, X-ray diffraction structure determination and analysis at 2.0-2.6 A resolution
Arabidopsis thaliana
Engineering
Amino acid exchange
Commentary
Organism
F218V
a mutant protein that produces the stereoisomer of primary fluorescent chlorophyll catabolites at the C1 position, the F218V mutation changes the stereospecificity in RCCR. Construction of wild-type and F218V mutant RCCR lacking the chloroplast transit peptide, Met1 to Gln39, i.e. RCCRDELTA49; the AtRCCR mutant protein produces the stereoisomer of primary fluorescent chlorophyll catabolites at the C1 position. The RCC in F218V AtRCCR rotates slightly compared with that in wild-type to fill in the space generated by the substitution of Phe218 with valine. Concomitantly, the two carboxy groups of Glu154 and Asp291 move slightly away from the C20/C1 double bond. Analysis of substrate-free and substrate-bound enzyme crystal structures, and comparison to wild-type structures, overview
Arabidopsis thaliana
additional information
construction of N-terminally truncated variants of wild-type enzyme and enzyme mutant F218V, i.e. AtRCCRDELTA49 and F218V AtRCCRDELTA49
Arabidopsis thaliana
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
chloroplast
stroma
Arabidopsis thaliana
9507
-
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
primary fluorescent chlorophyll catabolite + NADP+
Arabidopsis thaliana
stereospecific reaction. RCCR catalyzes the ferredoxin-dependent and site-specific reduction of the C20/C1 double bond of red chlorophyll catabolite, RCC, the catabolic intermediate produced in chlorophyll degradation
red chlorophyll catabolite + NADPH + H+
-
-
r
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
Arabidopsis thaliana
-
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Arabidopsis thaliana
Q8LDU4
-
-
Purification (Commentary)
Commentary
Organism
recombinant GST-tagged wild-type and F218V mutant RCCR lacking the chloroplast transit peptide, Met1 to Gln39, i.e. RCCRDELTA49; recombinant truncated wild-type and mutant enzymes AtRCCRDELTA49 and F218V AtRCCRDELTA49
Arabidopsis thaliana
Source Tissue
Source Tissue
Commentary
Organism
Textmining
leaf
-
Arabidopsis thaliana
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
primary fluorescent chlorophyll catabolite + NADP+
stereospecific reaction
712769
Arabidopsis thaliana
red chlorophyll catabolite + NADPH + H+
red chlorophyll catabolite, RCC, binding does not drastically change the RCCR structure, binding structure and mechanism analysis, overview. Comparison of the RCC-binding pockets of wild-type RCCRDELTA49 and F218V RCCRDELTA49, overview
-
-
r
primary fluorescent chlorophyll catabolite + NADP+
stereospecific reaction. RCCR catalyzes the ferredoxin-dependent and site-specific reduction of the C20/C1 double bond of red chlorophyll catabolite, RCC, the catabolic intermediate produced in chlorophyll degradation
712769
Arabidopsis thaliana
red chlorophyll catabolite + NADPH + H+
-
-
-
r
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
-
712769
Arabidopsis thaliana
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
-
-
-
?
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
loose substrate binding allows for conformation change during the reaction, stereospcific reaction, mechanism, overview
712769
Arabidopsis thaliana
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
formation of a stereospecific product, overview
-
-
?
Subunits
Subunits
Commentary
Organism
homodimer
RCCR folds into a characteristic alphabetaalpha sandwich
Arabidopsis thaliana
More
RCCR folds into a characteristic alpha/beta/alpha sandwich, similar to that observed in the ferredoxin-dependent bilin reductase family, structure comparisosns, overview
Arabidopsis thaliana
Cofactor
Cofactor
Commentary
Organism
Structure
Ferredoxin
dependent on
Arabidopsis thaliana
NADP+
-
Arabidopsis thaliana
NADPH
-
Arabidopsis thaliana
Cloned(Commentary) (protein specific)
Commentary
Organism
expression of GST-tagged wild-type and F218V mutant RCCR lacking the chloroplast transit peptide, Met1 to Gln39; expression of wild-type and mutant enzymes lacking the chloroplast transit peptide (Met1 to Gln39) and N-termial residues 40-48 as GST-tagged enzymes
Arabidopsis thaliana
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
Ferredoxin
dependent on
Arabidopsis thaliana
NADP+
-
Arabidopsis thaliana
NADPH
-
Arabidopsis thaliana
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant RCC-bound wild-type enzyme AtRCCRDELTA49, RCC-bound and substrate-free enzyme mutant F218V AtRCCRDELTA49, sitting-drop vapor diffusion method, mixing of 10 mg/ml substrate-free and substrate-bound proteins in 20 mM Tris-HCl, pH 7.4, and 200 mM NaCl, with an equal volume of reservoir solution containing 30% or 35%, respectively, w/v PEG 2000 monomethyl ether, 0.1 M ammonium acetate, 3% v/v dioxane, and 0.1 M 4-morpholineethanesulfonic acid-NaOH, pH 6.5, equilibration gainst reservoir solution, 20°C, 1 day, X-ray diffraction structure determination and analysis at 2.0-2.6 A resolution; purified recombinant red chlorophyll catabolite-bound RCCRDELTA49, and red chlorophyll catabolite-bound or substrate-free F218V RCCRDELTA49, sitting drop vapor diffusion method, 20°C, protein solution is mixed with an equal volume of reservoir solution and equilibrated against reservoir solution containing 30% w/v PEG 2000 monomethyl ether, 0.1 M ammonium acetate, 3% v/v dioxane, and 0.1 M 4-morpholineethanesulfonic acid-NaOH, pH 6.5, 1 day, X-ray diffraction structure determination and analysis at 2.0-2.6 A resolution
Arabidopsis thaliana
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
F218V
a mutant protein that produces the stereoisomer of primary fluorescent chlorophyll catabolites at the C1 position, the F218V mutation changes the stereospecificity in RCCR. Construction of wild-type and F218V mutant RCCR lacking the chloroplast transit peptide, Met1 to Gln39, i.e. RCCRDELTA49; the AtRCCR mutant protein produces the stereoisomer of primary fluorescent chlorophyll catabolites at the C1 position. The RCC in F218V AtRCCR rotates slightly compared with that in wild-type to fill in the space generated by the substitution of Phe218 with valine. Concomitantly, the two carboxy groups of Glu154 and Asp291 move slightly away from the C20/C1 double bond. Analysis of substrate-free and substrate-bound enzyme crystal structures, and comparison to wild-type structures, overview
Arabidopsis thaliana
additional information
construction of N-terminally truncated variants of wild-type enzyme and enzyme mutant F218V, i.e. AtRCCRDELTA49 and F218V AtRCCRDELTA49
Arabidopsis thaliana
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
chloroplast
stroma
Arabidopsis thaliana
9507
-
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
primary fluorescent chlorophyll catabolite + NADP+
Arabidopsis thaliana
stereospecific reaction. RCCR catalyzes the ferredoxin-dependent and site-specific reduction of the C20/C1 double bond of red chlorophyll catabolite, RCC, the catabolic intermediate produced in chlorophyll degradation
red chlorophyll catabolite + NADPH + H+
-
-
r
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
Arabidopsis thaliana
-
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant GST-tagged wild-type and F218V mutant RCCR lacking the chloroplast transit peptide, Met1 to Gln39, i.e. RCCRDELTA49; recombinant truncated wild-type and mutant enzymes AtRCCRDELTA49 and F218V AtRCCRDELTA49
Arabidopsis thaliana
Source Tissue (protein specific)
Source Tissue
Commentary
Organism
Textmining
leaf
-
Arabidopsis thaliana
-
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
primary fluorescent chlorophyll catabolite + NADP+
stereospecific reaction
712769
Arabidopsis thaliana
red chlorophyll catabolite + NADPH + H+
red chlorophyll catabolite, RCC, binding does not drastically change the RCCR structure, binding structure and mechanism analysis, overview. Comparison of the RCC-binding pockets of wild-type RCCRDELTA49 and F218V RCCRDELTA49, overview
-
-
r
primary fluorescent chlorophyll catabolite + NADP+
stereospecific reaction. RCCR catalyzes the ferredoxin-dependent and site-specific reduction of the C20/C1 double bond of red chlorophyll catabolite, RCC, the catabolic intermediate produced in chlorophyll degradation
712769
Arabidopsis thaliana
red chlorophyll catabolite + NADPH + H+
-
-
-
r
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
-
712769
Arabidopsis thaliana
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
-
-
-
?
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
loose substrate binding allows for conformation change during the reaction, stereospcific reaction, mechanism, overview
712769
Arabidopsis thaliana
primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster
formation of a stereospecific product, overview
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
homodimer
RCCR folds into a characteristic alphabetaalpha sandwich
Arabidopsis thaliana
More
RCCR folds into a characteristic alpha/beta/alpha sandwich, similar to that observed in the ferredoxin-dependent bilin reductase family, structure comparisosns, overview
Arabidopsis thaliana
General Information
General Information
Commentary
Organism
evolution
the enzyme belongs to the ferredoxin-dependent bilin reductase (FDBR) family. RCC is bound to the pocket between the beta-sheet and the C-terminal alpha-helices, as seen in substrate-bound FDBRs, but RCC binding to RCCR is much looser than substrate binding to FDBRs
Arabidopsis thaliana
additional information
the substrate red chlorophyll catabolite is bound to the pocket between the beta-sheet and the C-terminal alpha-helices. Substrate RCC binds quiet lossely to the enzyme. The loose binding seems beneficial to the large conformational change in red chlorophyll catabolite upon reduction. Two conserved acidic residues, Glu154 and Asp291, sandwich the C20/C1 double bond of RCC, suggesting that these two residues are involved in site-specific reduction. The geometrical arrangement of RCC and the carboxy groups of Glu154 and Asp291 in RCCR is essential for the stereospecificity of the RCCR reaction, substrate binding mechanism, overview. Analysis of substrate-free and substrate-bound enzyme crystal structures, and comparison to F218V enzyme mutant structures, overview
Arabidopsis thaliana
physiological function
red chlorophyll catabolite reductase (RCCR) catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite (RCC), the catabolic intermediate produced in chlorophyll degradation
Arabidopsis thaliana
General Information (protein specific)
General Information
Commentary
Organism
evolution
the enzyme belongs to the ferredoxin-dependent bilin reductase (FDBR) family. RCC is bound to the pocket between the beta-sheet and the C-terminal alpha-helices, as seen in substrate-bound FDBRs, but RCC binding to RCCR is much looser than substrate binding to FDBRs
Arabidopsis thaliana
additional information
the substrate red chlorophyll catabolite is bound to the pocket between the beta-sheet and the C-terminal alpha-helices. Substrate RCC binds quiet lossely to the enzyme. The loose binding seems beneficial to the large conformational change in red chlorophyll catabolite upon reduction. Two conserved acidic residues, Glu154 and Asp291, sandwich the C20/C1 double bond of RCC, suggesting that these two residues are involved in site-specific reduction. The geometrical arrangement of RCC and the carboxy groups of Glu154 and Asp291 in RCCR is essential for the stereospecificity of the RCCR reaction, substrate binding mechanism, overview. Analysis of substrate-free and substrate-bound enzyme crystal structures, and comparison to F218V enzyme mutant structures, overview
Arabidopsis thaliana
physiological function
red chlorophyll catabolite reductase (RCCR) catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite (RCC), the catabolic intermediate produced in chlorophyll degradation
Arabidopsis thaliana
Other publictions for EC 1.3.7.12
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)
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1
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726323
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Nitric oxide deficiency accele ...
Arabidopsis thaliana
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8
e56345
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726877
Sakuraba
7-Hydroxymethyl chlorophyll a ...
Arabidopsis thaliana
Biochem. Biophys. Res. Commun.
430
32-37
2013
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1
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726165
Sakuraba
STAY-GREEN and chlorophyll cat ...
Arabidopsis thaliana
Plant Cell
24
507-518
2012
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1
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736688
Zhang
Correlation of leaf senescence ...
Brassica rapa
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168
2081-2087
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1
1
2
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712769
Sugishima
Crystal structures of the subs ...
Arabidopsis thaliana
J. Mol. Biol.
402
879-891
2010
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699585
Sugishima
Crystal structure of red chlor ...
Arabidopsis thaliana
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389
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2009
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700695
Ougham
The control of chlorophyll cat ...
Arabidopsis thaliana
Plant Biol.
10 Suppl 1
4-14
2008
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2
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676436
Pruzinska
In vivo participation of red c ...
Arabidopsis thaliana
Plant Cell
19
369-387
2007
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671354
Hörtensteiner
Chlorophyll degradation during ...
Arabidopsis sp., Hordeum vulgare, Solanum lycopersicum, Spinacia oleracea
Annu. Rev. Plant Biol.
57
55-77
2006
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3
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735438
Hoertensteiner
Chlorophyll degradation during ...
Arabidopsis thaliana
Annu. Plant Biol.
57
55-77
2006
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1
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1
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676587
Pruzinska
Chlorophyll breakdown in senes ...
Arabidopsis thaliana
Plant Physiol.
139
52-63
2005
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736960
Roca
Analysis of the chlorophyll ca ...
Lolium temulentum
Phytochemistry
65
1231-1238
2004
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