Literature summary for 1.3.7.12 extracted from

Sugishima, M.; Kitamori, Y.; Noguchi, M.; Kohchi, T.; Fukuyama, K.
Crystal structure of red chlorophyll catabolite reductase: enlargement of the ferredoxin-dependent bilin reductase family (2009), J. Mol. Biol., 389, 376-387.

Activating Compound

Activating Compound	Comment	Organism	Structure
additional information	the catalytic activity of RCCR in vitro dramatically increases by coupling with pheophorbide alpha oxygenase, which also results in a stereospecific product	Arabidopsis thaliana
additional information	the catalytic activity of RCCR in vitro dramatically increases by coupling with PaO, possibly due to cooperative action, although PaO has been localized to the plastid envelope and RCCR is a soluble stroma enzyme	Arabidopsis thaliana

Cloned(Commentary)

Cloned (Comment)	Organism
cloning and expression in Escherichia coli	Arabidopsis thaliana

Crystallization (Commentary)

Crystallization (Comment)	Organism
at 2.4 A resolution, determination of the crystal structure of, where chloroplast transit peptide is truncated and a Gly-Pro-Leu-Gly-Ser peptide is added to the N terminus, 2 peptide chains A and B are located in an asymmetric unit of the selenomethionine-RCCR crystal, these 2 chains form a homodimer, AtRCCR folds into an alpha/beta/alpha sandwich: 5 N-terminal alpha-helices, an anti-parallel beta-sheet consisting of 8 strands, and 4 C-terminal alpha-helices	Arabidopsis thaliana
purified substrate-free enzyme, with the chloroplast transit peptide truncated and a Gly-Pro-Leu-Gly-Ser peptide added to the N-terminus, X-ray diffraction structure determination and analysis at 2.5-2.7 A resolution, structure modelling	Arabidopsis thaliana

Crystallization (Comment)

Organism

at 2.4 A resolution, determination of the crystal structure of, where chloroplast transit peptide is truncated and a Gly-Pro-Leu-Gly-Ser peptide is added to the N terminus, 2 peptide chains A and B are located in an asymmetric unit of the selenomethionine-RCCR crystal, these 2 chains form a homodimer, AtRCCR folds into an alpha/beta/alpha sandwich: 5 N-terminal alpha-helices, an anti-parallel beta-sheet consisting of 8 strands, and 4 C-terminal alpha-helices

Arabidopsis thaliana

purified substrate-free enzyme, with the chloroplast transit peptide truncated and a Gly-Pro-Leu-Gly-Ser peptide added to the N-terminus, X-ray diffraction structure determination and analysis at 2.5-2.7 A resolution, structure modelling

Arabidopsis thaliana

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
chloroplast	mainly	Arabidopsis thaliana	9507	-
chloroplast	stroma, constitutive enzyme, the N-terminal 39-amino-acid stretch of RCCR is predicted to be the chloroplast transit peptide	Arabidopsis thaliana	9507	-
mitochondrion	in young seedlings and in response to stress, RCCR is somewhat localized to mitochondria	Arabidopsis thaliana	5739	-
additional information	RCCR is constitutively expressed in chloroplasts, whereas in young seedlings and in response to stress, it is also localized to mitochondria	Arabidopsis thaliana	-	-

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
32000	-	2 * 32000, predicted by amino acid sequence, each subunit folds in an alpha/beta/alpha sandwich	Arabidopsis thaliana
32000	-	2 * 32000, about, sequence calculation	Arabidopsis thaliana
60000	-	about, gel filtration	Arabidopsis thaliana
60000	-	dimer, determined by gel filtration	Arabidopsis thaliana

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+	Arabidopsis thaliana	-	primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster	-	?
red chlorophyll catabolite + reduced acceptor	Arabidopsis thaliana	the key steps in the degradation pathway of chlorophylls are the ring-opening reaction catalyzed by pheophorbide a oxygenase and sequential reduction by RCCR, RCCR catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite	primary fluorescent chlorophyll catabolite + oxidized acceptor	in the acidic environment of vacuoles, primary fluorescent chlorophyll catabolite is spontaneously converted into nonfluorescent chlorophyll catabolites	?

Organism

Organism	UniProt	Comment	Textmining
Arabidopsis thaliana	Q8LDU4	-	-

Purification (Commentary)

Purification (Comment)	Organism
anion exchange chromatography	Arabidopsis thaliana

Source Tissue

Source Tissue	Comment	Organism	Textmining
leaf	-	Arabidopsis thaliana	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+	-	Arabidopsis thaliana	primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster	-	?
red chlorophyll catabolite + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+	-	Arabidopsis thaliana	primary fluorescent chlorophyll catabolite + 2 oxidized ferredoxin [iron-sulfur] cluster	formation of a stereospecific product, overview	?
red chlorophyll catabolite + reduced acceptor	the key steps in the degradation pathway of chlorophylls are the ring-opening reaction catalyzed by pheophorbide a oxygenase and sequential reduction by RCCR, RCCR catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite	Arabidopsis thaliana	primary fluorescent chlorophyll catabolite + oxidized acceptor	in the acidic environment of vacuoles, primary fluorescent chlorophyll catabolite is spontaneously converted into nonfluorescent chlorophyll catabolites	?

Subunits

Subunits	Comment	Organism
homodimer	2 * 32000, predicted by amino acid sequence, each subunit folds in an alpha/beta/alpha sandwich	Arabidopsis thaliana
homodimer	2 * 32000, about, sequence calculation	Arabidopsis thaliana
More	enzyme RCCR forms a homodimer, in which each subunit folds in an alphabetaalpha sandwich, five N-terminal alpha-helices (H1/H2/H3/H5/H7), an anti-parallel beta-sheet consisting of eight strands (S1-S8), and four C-terminal alpha-helices (H4/H6/H8/H9). The two subunits are related by noncrystallographic 2fold symmetry in which the alpha-helices near the edge of the beta-sheet unique in RCCR participate in intersubunit interaction. The putative RCC-binding site forms an open pocket surrounded by conserved residues among RCCRs. Residues Glu154 and Asp291 stand opposite each other in the substrate binding pocket and are likely involved in substrate binding and/or catalysis. Primary structure comparisons, overview	Arabidopsis thaliana

Synonyms

Synonyms	Comment	Organism
RCCR	-	Arabidopsis thaliana
red chlorophyll catabolite reductase	-	Arabidopsis thaliana

Cofactor

Cofactor	Comment	Organism	Structure
Ferredoxin	-	Arabidopsis thaliana
Ferredoxin	dependent on	Arabidopsis thaliana

General Information

General Information	Comment	Organism
evolution	the enzyme belongs to the ferredoxin-dependent bilin reductase (FDBR) family, which synthesizes a variety of phytobilin pigments, on the basis of sequence similarity, ferredoxin dependency, and the common tetrapyrrole skeleton of their substrates. The tertiary structure of RCCR is similar to those of FDBRs, strongly supporting that these enzymes evolved from a common ancestor	Arabidopsis thaliana
additional information	Residues Glu154 and Asp291 stand opposite each other in the substrate binding pocket and are likely involved in substrate binding and/or catalysis	Arabidopsis thaliana
physiological function	the key steps in the degradation pathway of chlorophylls are the ring opening reaction catalyzed by pheophorbide a oxygenase and sequential reduction by red chlorophyll catabolite reductase (RCCR). During these steps, chlorophyll catabolites lose their color and phototoxicity. Enzyme RCCR catalyzes the ferredoxin-dependent reduction of the C20/C1 double bond of red chlorophyll catabolite	Arabidopsis thaliana