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Information on EC 1.14.13.81 - magnesium-protoporphyrin IX monomethyl ester (oxidative) cyclase and Organism(s) Rubrivivax gelatinosus and UniProt Accession P0DJN9

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EC Tree
IUBMB Comments
Requires Fe(II) for activity. The enzyme participates in the biosynthesis of chlorophyllide a in aerobic organisms. The same transformation is achieved in anaerobic organisms by EC 1.21.98.3, anaerobic magnesium-protoporphyrin IX monomethyl ester cyclase. Some facultative phototrophic bacteria, such as Rubrivivax gelatinosus, possess both enzymes.
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This record set is specific for:
Rubrivivax gelatinosus
UNIPROT: P0DJN9
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Word Map
The taxonomic range for the selected organisms is: Rubrivivax gelatinosus
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
Synonyms
chl27, mg-protoporphyrin ix monomethyl ester cyclase, xantha-l, pempec, mg-protoporphyrin ix monomethyl ester (oxidative) cyclase, sll1214, mg protoporphyrin monomethylester cyclase, oscrd1, mpe-cyclase, magnesium-protoporphyrin ix monomethyl ester cyclase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
AcsF protein
previously named orf358
magnesium-protoporphyrin IX monomethyl ester cyclase
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Mg-protoporphyrin IX monomethyl ester cyclase
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MPEC gene product
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O2-dependent Mg-protoporphyrin monomethyl ester cyclase
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cyclase, magnesium protoporphyrin IX monomethyl ester
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magnesium-protoporphyrin-IX monomethyl ester cyclase
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magnesium-protoporphyrin-IX monomethyl ester oxidative cyclase
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Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase
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Mg-protoporphyrin monomethylester cyclase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
magnesium-protoporphyrin IX 13-monomethyl ester + 3 NADPH + 3 H+ + 3 O2 = 3,8-divinyl protochlorophyllide a + 3 NADP+ + 5 H2O
show the reaction diagram
mass spectrometry identified 131-hydroxy-MgPME and 131-keto-MgPME are intermediates in the formation of the isocyclic ring, revealing the reaction chemistry that converts porphyrins to chlorins. Reaction mechanism, identification of proposed reaction intermediates in the progress of the reaction by mass spectrometry, overview
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
cyclization
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redox reaction
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oxidation
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reduction
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SYSTEMATIC NAME
IUBMB Comments
magnesium-protoporphyrin-IX 13-monomethyl ester,NADPH:oxygen oxidoreductase (hydroxylating)
Requires Fe(II) for activity. The enzyme participates in the biosynthesis of chlorophyllide a in aerobic organisms. The same transformation is achieved in anaerobic organisms by EC 1.21.98.3, anaerobic magnesium-protoporphyrin IX monomethyl ester cyclase. Some facultative phototrophic bacteria, such as Rubrivivax gelatinosus, possess both enzymes.
CAS REGISTRY NUMBER
COMMENTARY hide
92353-62-3
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
magnesium-protoporphyrin IX 13-monomethyl ester + 3 NADPH + 3 H+ + 3 O2
3,8-divinyl protochlorophyllide a + 3 NADP+ + 5 H2O
show the reaction diagram
overall reaction
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-
?
magnesium-protoporphyrin IX monomethyl ester + NADPH + H+ + O2
protochlorophyllide a + NADP+ + H2O
show the reaction diagram
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intermediates are 6-beta-hydroxy analogue and 6-beta-oxo analogue of protochlorophyllide a
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?
magnesium-protoporphyrin IX monomethyl ester + NADPH + O2
magnesium-divinyl-protochlorophyllide + NADP+ + H2O
show the reaction diagram
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?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
magnesium-protoporphyrin IX 13-monomethyl ester + 3 NADPH + 3 H+ + 3 O2
3,8-divinyl protochlorophyllide a + 3 NADP+ + 5 H2O
show the reaction diagram
overall reaction
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-
?
magnesium-protoporphyrin IX monomethyl ester + NADPH + H+ + O2
protochlorophyllide a + NADP+ + H2O
show the reaction diagram
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intermediates are 6-beta-hydroxy analogue and 6-beta-oxo analogue of protochlorophyllide a
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?
magnesium-protoporphyrin IX monomethyl ester + NADPH + O2
magnesium-divinyl-protochlorophyllide + NADP+ + H2O
show the reaction diagram
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADPH
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe2+
required, presence of a diiron cluster in AcsF
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0073 - 0.16
magnesium-protoporphyrin IX 13-monomethyl ester
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0151 - 0.0177
magnesium-protoporphyrin IX 13-monomethyl ester
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.111 - 2.069
magnesium-protoporphyrin IX 13-monomethyl ester
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
in photosynthetic tissue, undetectable in non-photosynthetic tissues
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the process for the formation of the unique isocyclic fifth ring of chlorophyll involves the conversion of Mg-protoporphyrin IX monomethyl ester (MgPME) to 3,8-divinyl protochlorophyllide a (DV PChlide a), and it requires incorporation of an oxygen atom, sourced from either water or O2, indicating the existence of two mechanistically different MgPME cyclases. Most anoxygenic phototrophic bacteria utilise an O2-sensitive radical SAM enzyme containing [4Fe-4S] and cobalamin cofactors to catalyse the reaction, while oxygenic phototrophs including cyanobacteria, algae and plants, as well as some purple bacteria, adopt an O2-dependent cyclase for the reaction. Mg-protoporphyrin IX monomethyl ester (MgPME) cyclase catalyses the formation of the isocyclic ring, the hallmark of chlorins and bacteriochlorins, producing protochlorophyllide a and contributing significantly to the absorption properties of chlorophylls and bacteriochlorophylls. Three classes of O2-dependent cyclase have been identified, all with a catalytic subunit AcsF, a putative diiron protein, but they differ in the requirement for an auxiliary subunit, either Ycf54 for the enzyme found in oxygenic phototrophs, or BciE for the alphaproteobacterial enzyme
malfunction
a Rubrivivax gelatinosus strain with disrupted acsF gene cannot synthesize bacteriochlorophyll under oxygenated conditions but accumulates the substrate magnesium-protoporphyrin IX monomethyl ester, in contrast, under low-oxygene conditions the phenotype is similar to the wild-type, an alternative pathway for the reaction exists vie the bchE genes
metabolism
protochlorophyllide a production (formation of the isocyclic ring) via several intermediates in the chlorophyll biosynthesis pathway
physiological function
cyclic tetrapyrroles, are among the most abundant natural pigments on Earth. They are the major absorbers of the solar energy that drives photosynthesis, and billions of tonnes of chlorophyll are synthesised annually on land and in the oceans. The decisive biosynthetic step that determines the absorption properties of chlorophyll, and more visually its green color, is the formation of the unique isocyclic fifth ring. This process involves the conversion of Mg-protoporphyrin IX monomethyl ester (MgPME) to 3,8-divinyl protochlorophyllide a (DV PChlide a), and it requires incorporation of an oxygen atom, sourced from either water or O2, indicating the existence of two mechanistically different MgPME cyclases. Most anoxygenic phototrophic bacteria utilise an O2-sensitive radical SAM enzyme containing [4Fe-4S] and cobalamin cofactors to catalyse the reaction, while oxygenic phototrophs including cyanobacteria, algae and plants, as well as some purple bacteria, adopt an O2-dependent cyclase for the reaction. Mg-protoporphyrin IX monomethyl ester (MgPME) cyclase catalyses the formation of the isocyclic ring, the hallmark of chlorins and bacteriochlorins, producing protochlorophyllide a and contributing significantly to the absorption properties of chlorophylls and bacteriochlorophylls. The diiron cluster within AcsF is reduced by ferredoxin furnished by NADPH and ferredoxin:NADP+ reductase or by direct coupling to Photosystem I photochemistry, linking cyclase to the photosynthetic electron transport chain
metabolism
magnesium-protoporphyrin IX monomethylester cyclase is one of the key enzymes of the bacteriochlorophyll biosynthesis pathway
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
ACSF_RUBGE
358
0
41513
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
210000
detergent solubilized, purified recombinant His6-tagged enzyme, gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer or trimer
x * 37000, recombinant enzyme, SDS-PAGE, x * 44000, sequence calculation
heterodimer
2 * ?, highly conserved leucin zipper domain and EXnEXRH motif (binding binuclear-iron cluster)
additional information
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
57.2
the melting point of AcsF
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
single-subunit O2-dependent cyclase AcsF, recombinant N-terminally His6-tagged enzyme from Escherichia coli strain C43(DE3) by nickel affinity chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene acsF, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli strain C43(DE3)
RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
iron reconstitution step with ferrous ammonium sulphate to increase the occupancy of the iron-binding sites, the purified single-subunit O2-dependent cyclase AcsF activity is reconstituted using a tricomponent electron transfer system consisting of NADPH, ferredoxin (Fd) and Fd:NADP+ reductase (FNR)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Liu, H.; Zheng, C.
MPEC: An important gene in the chlorophyll biosynthesis pathway in photosynthetic organisms
Photosynthetica
46
321-328
2008
Arabidopsis thaliana (Q9M591), Brassica napus (Q7XJI2), Chlamydomonas reinhardtii (Q9AR22), Chlamydomonas reinhardtii (Q9LD46), Cucumis sativus, Hordeum vulgare (Q5EFU4), Ipomoea nil (Q40093), Nicotiana tabacum, Oryza sativa, Rosa davurica, Rubrivivax gelatinosus (P0DJN9), Salix babylonica (Q7XJI4), Spinacia oleracea (Q7XJI5), Trifolium repens (Q7XJI1), Triticum aestivum (Q7XJI6)
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Manually annotated by BRENDA team
Boldareva-Nuianzina, E.N.; Blahova, Z.; Sobotka, R.; Koblizek, M.
Distribution and origin of oxygen-dependent and oxygen-independent forms of Mg-protoporphyrin monomethylester cyclase among phototrophic proteobacteria
Appl. Environ. Microbiol.
79
2596-2604
2013
Acidiphilium multivorum (F0IZP3), Acidiphilium multivorum AIU301 (F0IZP3), Agrobacterium albertimagni (K2PJ79), Agrobacterium albertimagni AOL15 (K2PJ79), Ahrensia sp. R2A130 (E0MPX4), Bradyrhizobium sp., Bradyrhizobium sp. BTAi1, Bradyrhizobium sp. ORS278, Brevundimonas subvibrioides (D9QPB7), Brevundimonas subvibrioides ATCC 15264 (D9QPB7), Cereibacter sphaeroides, Citromicrobium bathyomarinum, Citromicrobium bathyomarinum JL354, Congregibacter litoralis (A4ACN5), Congregibacter litoralis KT71 (A4ACN5), Dinoroseobacter shibae (A8LQ37), Dinoroseobacter shibae DFL 12 (A8LQ37), Erythrobacter sp. (A3WHT4), Erythrobacter sp. NAP1 (A3WHT4), gamma proteobacterium HIMB55 (H3NRI3), gammaproteobacteria, gammaproteobacteria HTCC2080, gammaproteobacteria NOR5-3, gammaproteobacteria NOR51-B, Hoeflea phototrophica (A9DA86), Hoeflea phototrophica DFL-43 (A9DA86), Jannaschia sp. CCS1 (Q28W44), Limnohabitans sp., Limnohabitans sp. Rim28, Limnohabitans sp. Rim47, Methylobacterium radiotolerans, Methylobacterium sp., Methylobacterium sp. 4-46, Methylocella silvestris, Methylocella silvestris BL2, Methylorubrum extorquens (C5AV79), Methylorubrum extorquens ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 (C5AV79), Methylorubrum populi (B1ZBN5), Methylorubrum populi BJ001 (B1ZBN5), Methyloversatilis universalis (F5RI16), Methyloversatilis universalis FAM5 (F5RI16), Rhodobacter sp. (C8RYM0), Rhodomicrobium vannielii, Rhodomicrobium vannielii ATCC 17100, Rhodopseudomonas palustris, Rhodospirillum centenum (B6ITV8), Roseibium alexandrii (A0A5E8GWV2), Roseibium alexandrii DFL-11 (A0A5E8GWV2), Roseobacter denitrificans (Q16DS9), Roseobacter litoralis, Roseobacter litoralis Och 149c, Roseobacter sp. (A4EGS5), Roseobacter sp. (A6FPX8), Roseobacter sp. AzwK-3b (A6FPX8), Roseovarius sp., Roseovarius sp. (A3VXW7), Roseovarius sp. TM1035, Rubrivivax benzoatilyticus (F3LQD6), Rubrivivax benzoatilyticus JA2 (F3LQD6), Rubrivivax gelatinosus (I0HUK7), Rubrivivax gelatinosus IL144 (I0HUK7), Sphingomonas sp., Yoonia vestfoldensis (A3V2J0), Yoonia vestfoldensis SKA53 (A3V2J0), Roseobacter sp. CCS2 (A4EGS5), Roseovarius sp. 217 (A3VXW7)
Manually annotated by BRENDA team
Chen, G.E.; Adams, N.B.P.; Jackson, P.J.; Dickman, M.J.; Hunter, C.N.
How the O2-dependent Mg-protoporphyrin monomethyl ester cyclase forms the fifth ring of chlorophylls
Nat. plants
7
365-375
2021
Rubrivivax gelatinosus (P0DJN9), Rubrivivax gelatinosus
Manually annotated by BRENDA team