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Information on EC 1.3.98.3 - coproporphyrinogen dehydrogenase
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1.3.98.3 coproporphyrinogen dehydrogenaseIUBMB Comments
This enzyme differs from EC 1.3.3.3, coproporphyrinogen oxidase, by using S-adenosyl-L-methionine (AdoMet) instead of oxygen as oxidant. It occurs mainly in bacteria, whereas eukaryotes use the oxygen-dependent oxidase. The reaction starts by using an electron from the reduced form of the enzyme's [4Fe-4S] cluster to split AdoMet into methionine and the radical 5'-deoxyadenosin-5'-yl. This radical initiates attack on the 2-carboxyethyl groups, leading to their conversion into vinyl groups. This conversion, ---(.)CH-CH2-COO- -> ---CH=CH2 + CO2 + e- replaces the electron initially used.
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Word Map
- 1.3.98.3
- viruses
-
interferon-inducible
- s-adenosylmethionine
-
interferon-stimulated
-
5\'-deoxyadenosyl
-
ifn-stimulated
- isg15
-
ifn-inducible
-
radical-mediated
-
polyi:c
-
myxovirus
-
ifitm3
- 5'-deoxyadenosine
-
maturase
- hydg
- protoporphyrinogen
-
chuat
-
siniperca
- medicine
- pharmacology
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
Synonyms
viperin, radical sam enzyme, oxygen-independent coproporphyrinogen iii oxidase, anaerobic coproporphyrinogen iii oxidase, athemn1, sll1876, sll1917, oxygen-independent cpo, oxygen-independent coproporphyrinogen-iii oxidase, at5g63290, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
anaerobic coproporphyrinogen III oxidase
BtrN
coproporphyrinogen III oxidase
CPO
EC 1.3.99.22
-
-
formerly
-
HemN
oxygen-independent coproporphyrinogen III oxidase
oxygen-independent coproporphyrinogen-III oxidase
additional information
BtrN
-
BtrN is an unusual radical SAM dehydrogenase catalyzing the oxidation of the hydroxyl group by a radical mechanism
oxygen-independent coproporphyrinogen III oxidase
-
-
oxygen-independent coproporphyrinogen III oxidase
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
mechanism
coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
catalytic, radical mechanism
-
coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
this enzyme differs from EC 1.3.3.3, coproporphyrinogen oxidase, by using S-adenosyl-L-methionine, AdoMet, instead of oxygen as oxidant, it occurs mainly in bacteria, whereas eukaryotes use the oxygen-dependent oxidase, the reaction starts by using an electron from the reduced form of the enzymes [4Fe-4S] cluster to split AdoMet into methionine and the radical 5-deoxyadenosin-5-yl, this radical initiates attack on the 2-carboxyethyl groups, leading to their conversion into vinyl groups. The conversion of .CH-CH2-COO- leading to CH=CH2 + CO2 + e- replaces the electron initially used, reaction mechanism
-
coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
conversion of coproporphyrinogen III to protoporphyrinogen IX via the reaction intermediate harderoporphyrinogen. HemN contains a catalytically essential [4Fe-4S] cluster that transfers an electron to bound S-adenosyl-L-methionine, thereby producing methionine and a 5'-deoxyadenosyl radical. This radical then abstracts a hydrogen atom from the beta-carbon of the substrate propionate side chain, resulting in the formation of a coproporphyrinogenyl radical, overview
-
coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
coproporphyrinogen-III:S-adenosyl-L-methionine oxidoreductase (decarboxylating)
This enzyme differs from EC 1.3.3.3, coproporphyrinogen oxidase, by using S-adenosyl-L-methionine (AdoMet) instead of oxygen as oxidant. It occurs mainly in bacteria, whereas eukaryotes use the oxygen-dependent oxidase. The reaction starts by using an electron from the reduced form of the enzyme's [4Fe-4S] cluster to split AdoMet into methionine and the radical 5'-deoxyadenosin-5'-yl. This radical initiates attack on the 2-carboxyethyl groups, leading to their conversion into vinyl groups. This conversion, ---(.)CH-CH2-COO- -> ---CH=CH2 + CO2 + e- replaces the electron initially used.
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CAS REGISTRY NUMBER
COMMENTARY
9076-84-0
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2-deoxy-scyllo-inosamine + S-adenosyl-L-methionine
3-amino-2,3-dideoxy-scyllo-inosose + CO2 + L-methionine + 5'-deoxyadenosine
2-deoxystreptamine + S-adenosyl-L-methionine
? + CO2 + L-methionine + 5'-deoxyadenosine
-
14.4% activity compared to 2-deoxy-scyllo-inosamine
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
coproporphyrinogen III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
harderoporphyrinogen + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
HemN can utilize chemically synthesized harderoporphyrinogen as a substrate and converts it to protoporphyrinogen IX
-
-
?
harderoporphyrinogen + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
chemical substrate sythesis, overview
-
-
?
myo-inositol + S-adenosyl-L-methionine
? + CO2 + L-methionine + 5'-deoxyadenosine
-
0.9% activity compared to 2-deoxy-scyllo-inosamine
-
-
?
scyllo-inositol + S-adenosyl-L-methionine
? + CO2 + L-methionine + 5'-deoxyadenosine
-
3.3% activity compared to 2-deoxy-scyllo-inosamine
-
-
?
2-deoxy-scyllo-inosamine + S-adenosyl-L-methionine
3-amino-2,3-dideoxy-scyllo-inosose + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
-
r
2-deoxy-scyllo-inosamine + S-adenosyl-L-methionine
3-amino-2,3-dideoxy-scyllo-inosose + CO2 + L-methionine + 5'-deoxyadenosine
-
100% activity
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
via reaction intermediate harderoporphyrinogen, not isoharderoporphyrinogen
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
via reaction intermediate harderoporphyrinogen, not isoharderoporphyrinogen. During this reaction the propionate side chains on pyrrole rings A and B of coproporphyrinogen III are oxidatively decarboxylated to the corresponding vinyl groups of protoporphyrinogen IX. Two molecules of CO2 are released during the reaction and a final electron acceptor is required to take up two electrons from each side chain
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
conversion of coproporphyrinogen III to protoporphyrinogen IX via the reaction intermediate harderoporphyrinogen
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
reductive cleavage of S-adenosyl-L-methionine to produce methionine and a 5'-deoxyadenosyl radical intermediate, a reaction characteristic of the radical SAM superfamily, due to the presence of a CX3CX2C motif
detection of the cleavage and degradation products and analysis by mass spectrometry, overview
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
sll1876 encodes HemN operating under micro-oxic conditions
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
only Sll1876 shows CPO activity under anaerobic conditions, Sll1917 is inactive
-
-
?
coproporphyrinogen III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
HemN catalyzes the essential conversion of coproporphyrinogen-III to protoporphyrinogen IX during heme biosynthesis
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
HemN catalyzes the prepenultimate step in anaerobic heme biosynthesis
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
HemN catalyzes the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen IX, requires S-adenosyl-L-methionine, NAD(P)H and additional cytoplasmatic components for catalysis. Cys-62, Cys-66 and Cys-69 are part of the conserved CXXXCXXC motif and essential for iron-sulfur cluster formation and enzyme function. Gly-111 and Gly-113 are part of the potential GGGTP S-adenosyl-L-methionine binding motif and essential for enzymatic function, catalytic, radical mechanism
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
HemN requires the juxtaposition of the [4Fe-4S] cluster and the cosubstrate S-adenosyl-L-methionine. The reaction involves the stereospecific hydrogen abstraction of the pro-S hydrogen from the propionate side chain beta-C of coproporphyrinogen-III, involvement of a coproporphyrinogenyl III radical, which is then decarboxylated releasing CO2 and forming the vinyl group, enzyme structure, two-domain enzyme consisting of the catalytic N- and an alpha-helical C-terminal domain, substrate binding mode
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
mechanism, the S-adenosyl-L-methionine sulfonium sulfur is near both the Fe and neighboring sulfur of the cluster allowing single electron transfer from the 4Fe-4S cluster to the S-adenosyl-L-methionine sulfonium. S-adenosyl-L-methionine is cleaved yielding a highly oxidizing 5-deoxyadenosyl radical, HemN binds a second S-adenosyl-L-methionine immediately adjacent to the first and may thus successively catalyze two propionate decarboxylations. Cofactor geometry required for Radical SAM catalysis, detailed enzyme structure, two distinct domains, domain structure, S-adenosyl-L-methionine binding mode
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
-
?
additional information
?
-
-
HemW shows no coproporphyrinogen III oxidase activity in vivo or in vitro
-
-
?
additional information
?
-
-
no activity with 1L-chiro-inositol, muco-inositol, allo-inositol, D-glucose, D-glucosamine, D-xylose, 1D-chiro-inositol, and 2,3-dideoxy-scyllo-inosose
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
coproporphyrinogen III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
additional information
?
-
-
HemW shows no coproporphyrinogen III oxidase activity in vivo or in vitro
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
via reaction intermediate harderoporphyrinogen, not isoharderoporphyrinogen
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen III + 2 S-adenosyl-L-methionine
protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
-
sll1876 encodes HemN operating under micro-oxic conditions
-
-
?
coproporphyrinogen III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
HemN catalyzes the essential conversion of coproporphyrinogen-III to protoporphyrinogen IX during heme biosynthesis
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
HemN catalyzes the prepenultimate step in anaerobic heme biosynthesis
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4Fe-4S-center
HemN binds a 4Fe-4S cluster through three cysteine residues: Cys-62, Cys-66 and Cys-69, a juxtaposed S-adenosyl-L-methionine coordinates the fourth Fe ion through its amide nitrogen and carboxylate oxygen, detailed binding mode, cofactor geometry required for Radical SAM catalysis
4Fe-4S-center
-
requirement, oxygen-sensitive Fe-S cluster, Cys-62, Cys-66 and Cys-69 are part of the conserved CXXXCXXC motif and essential for Fe-S cluster formation and enzyme function, Tyr-56 and His-58 are important for the Fe-S cluster integrity, His-58 may provide the fourth ligand besides the three cysteine residues
4Fe-4S-center
-
structure, location and coordination of the cofactor, HemN requires the juxtaposition of the [4Fe-4S] cluster and the cosubstrate S-adenosyl-L-methionine
heme
-
in vivo, HemW occurs as a heme-free cytosolic form, as well as a heme-containing membrane-associated form
S-adenosyl-L-methionine
HemN contains two S-adenosyl-L-methionine molecules as cofactors, detailed binding mode
S-adenosyl-L-methionine
-
HemN contains a catalytically essential [4Fe-4S] cluster that transfers an electron to bound S-adenosyl-L-methionine, thereby producing methionine and a 5'-deoxyadenosyl radical
S-adenosyl-L-methionine
HemN is a radical S-adenosyl-L-methionine and [4Fe-4S] containing enzyme
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Fe2+
-
HemN contains a catalytically essential [4Fe-4S] cluster that transfers an electron to bound S-adenosyl-L-methionine, thereby producing methionine and a 5'-deoxyadenosyl radical
Fe2+
HemN is a radical S-adenosyl-L-methionine and [4Fe-4S] containing enzyme
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
O2
O2 affects tetrapyrrole biosynthesis presumably at the level of the S-adenosyl-L-methionine and [4Fe-4S] containing HemN enzyme
Cu2+
Cu2+ affects tetrapyrrole biosynthesis presumably at the level of the S-adenosyl-L-methionine and [4Fe-4S] containing HemN enzyme, copper targets the 4Fe-4S clusters in the anaerobic enzyme
Cu2+
copper affects tetrapyrrole biosynthesis presumably at the level of the SAM and [4Fe-4S] containing HemN enzyme. Members of the radical SAM enzyme family are copper sensitive. The excess copper target in the tetrapyrrole pathway is the anaerobic coproporphyrinogen III oxidase [4Fe-4S] containing HemN
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.022
2-deoxy-scyllo-inosamine
-
in 50 mM HEPES-NaOH (pH 8.0) in the presence of 10 mM sodium dithionite at 28°C
0.31
S-adenosyl-L-methionine
-
apparent value, in the presence of sodium dithionite (10 mM), at room temperature
0.46
S-adenosyl-L-methionine
-
apparent value, in 50 mM HEPES-NaOH (pH 8.0) in the presence of 10 mM sodium dithionite at 28°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.038
2-deoxy-scyllo-inosamine
-
in 50 mM HEPES-NaOH (pH 8.0) in the presence of 10 mM sodium dithionite at 28°C
0.02
S-adenosyl-L-methionine
-
apparent value, in 50 mM HEPES-NaOH (pH 8.0) in the presence of 10 mM sodium dithionite at 28°C
0.022
S-adenosyl-L-methionine
-
apparent value, in the presence of sodium dithionite (10 mM), at room temperature
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
promoter and transcript analyses indicate that AtHEMN1 is expressed mainly in floral tissues and developing seeds
brenda
promoter and transcript analyses indicate that AtHEMN1 is expressed mainly in floral tissues and developing seeds
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
in vivo, HemW occurs as a heme-free cytosolic form, as well as a heme-containing membrane-associated form
brenda
-
in vivo, HemW occurs as a heme-free cytosolic form, as well as a heme-containing membrane-associated form
brenda
recombinant AtHEMN1-GFP fusion protein is targeted to mitochondria
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
evolution
-
HemW-like proteins form a distinct phylogenetic clade. It contains the four cysteine residues of the radical S-adenosyl-L-methionine enzyme motif of CPDH enzymes, structure comparisons, overview. The fourth cysteine residue of the Fe-S cluster motif of Escherichia coli HemN, CX3CX2CXC, is replaced by phenylalanine in HemW and related proteins
evolution
-
in eukaryotes and some bacteria, oxidative decarboxylation of coproporphyrinogen III is performed by the oxygen-dependent CPO HemF, EC 1.3.3.3. In most bacteria, the reaction is catalyzed by the oxygen-independent enzyme HemN. HemN belongs to the family of radical S-adenosyl-L-methionine enzymes. HemF and HemN are structurally completely unrelated and show different catalytic mechanisms, overview
evolution
the anaerobic [4Fe-4S] containing enzymes have been replaced in metabolic pathways by more efficient and stable aerobic versions as a response and adaptation to oxygen appearance on earth, with copper damages [4Fe-4S] cluster under anaerobiosis or limited oxygen tensionplaying a role in the selection pressure leading to the evolution of copper/oxygen tolerant enzymes, copper targets the 4Fe-4S clusters in the anaerobic enzymes
malfunction
oxidized coproporphyrinogen III accumulates in a hemN2- mutant in Rubrivirax gelatinosus only under oxygen limited conditions
malfunction
excess copper in the copA- mutant, deficient for Cu+-ATPase CopA via transposon mutagenesis, results in a substantial decrease of the cytochrome c oxidase and the photosystem under microaerobic and anaerobic conditions together with the extrusion of coproporphyrin III. Enzyme CopA is required for the activity of cuproproteins in the purple bacterium Rubrivivax gelatinosus. CopA is not directly required for cytochrome c oxidase activity but is vital for copper tolerance. The Cu+-ATPase CtpA is required only for the activity of cuproproteins in the purple bacterium Rubrivivax gelatinosus
malfunction
mutation in Arabidopsis thaliana CPO-coding gene AtHEMN1 adversely affects silique length, ovule number, and seed set. T-DNA insertions in gene HEMN1 cause seed sterility. Athemn1 mutant alleles are transmitted via both male and female gametes, but homozygous mutants are never recovered. Plants carrying Athemn1 mutant alleles show defects in gametophyte development, including nonviable pollen and embryo sacs with unfused polar nuclei. Improper differentiation of the central cell leads to defects in endosperm development. Consequently, embryo development is arrested at the globular stage. Reactive oxygen species Accumulates around the central cell in the female gametophytes. The mutant phenotype is completely rescued by transgenic expression of AtHEMN1. Blockage of tetrapyrrole biosynthesis in the AtHEMN1 mutant leads to increased reactive oxygen species accumulation in anthers and embryo sacs. The accumulated reactive oxygen species disrupt mitochondrial function by altering their membrane polarity in floral tissues. The AtHEMN1 mutation prevents the fusion of polar nuclei in the female gametophyte and affects endosperm proliferation. T-DNA insertion mutant lines of Arabidopsis thaliana show bushy habit and short siliques. Cell specification is not affected in Athemn1-1 mutant embryo sacs. Phenotype, overview
metabolism
-
genes hemH and hemW (hemN) show conjectured functions in heme metabolism
metabolism
the enzyme is involved in the O2-independent tetrapyrrole biosynthesis pathway, regulation overview
metabolism
the enzyme plays an important role in the tetrapyrrole biosynthesis pathway in plants, overview
physiological function
-
catalyzes the decarboxylation of coproporphyrinogen III to form protoporphyrinogen IX in heme biosynthesis and is shared in chlorophyll biosynthesis in photosynthetic organisms
physiological function
-
viperin is an interferon-inducible protein inhibiting a diverse spectrum of DNA and RNA viruses. It contains an N-terminal transmembrane helix, a highly conserved C-terminus and a middle region carrying a CX3CX2C motif, characteristic of radical S-adenosyl-L-methionine enzymes. The radical SAM enzyme activity may play a key role in the broad antiviral actions of viperin
physiological function
-
addition of Lactococcus lactis membranes to heme-containing HemW triggers the release of heme from HemW in vitro. Role of HemW in heme trafficking
physiological function
coproporphyrinogen III is converted to protoporphyrinogen IX under anaerobiosis and low oxygen tension by the anaerobic coproporphyrinogen III oxidase HemN. The Cu+-ATPase CopA is not directly required for cytochrome c oxidase but is vital for copper tolerance. The physiological role of the copper P1B-type transporter CtpA, though homologous to CopA, differs from that of the effluxATPase CopA, because CtpA is dispensable for copper tolerance in contrast to CopA. HemN, a radical SAM and iron-sulfur containing protein, is a target enzyme in the tetrapyrrole biosynthesis pathway
physiological function
tetrapyrrole biosynthesis is one of the most essential metabolic pathways in almost all organisms. Coproporphyrinogen III oxidase catalyzes the oxidative decarboxylation of coproporphyrinogen III (coprogen) to yield protoporphyrinogen IX (protogen) in the tetrapyrrole biosynthesis pathway
additional information
-
the interferon-inducible antiviral protein viperin is a radical SAM enzyme, immune response pathway involving viperin that leads to the disruption of viral release from the plasma membrane, overview
additional information
a mutant Rubrivivax gelatinosus deficient in the Cu2+-ATPase CopA accumulates coproporphyrinogen III, excess copper affects the synthesis of tetrapyrroles, affecting the heme and chlorophyll containing complexes
additional information
-
a mutant Rubrivivax gelatinosus deficient in the Cu2+-ATPase CopA accumulates coproporphyrinogen III, excess copper affects the synthesis of tetrapyrroles, affecting the heme and chlorophyll containing complexes
Show AA Sequence and Transmembrane Helices (19375 entries)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
additional information
-
structure analysis of recombinant His-tagged viperin (214-361) by UV-visible, circular dichroism, and NMR spectroscopy, overview
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure, co-crystallized with S-adenosyl-L-methionine, hanging-drop vapor diffusion method, X-ray analysis
presence of an unusually coordinated iron-sulfur cluster and two molecules of S-adenosylmethionine, which is of functional importance
-
under strictly anaerobic conditions, comparison of the crystal structures of the three radical SAM enzymes HemN, BioB and MoaA show that the enzymes are structurally significantly different
-
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E145A
-
appears colorless, the [4Fe-4S] cluster content is slightly reduced, no detectable S-adenosylmethionine cleavage, no detectable CPO activity
E145I
-
appears colorless, the [4Fe-4S] cluster content is slightly reduced, no detectable S-adenosylmethionine cleavage, no detectable CPO activity
F310A
-
is slightly yellow, the [4Fe-4S] cluster content is slightly reduced, cleaves only one S-adenosylmethionine molecule per molecule protein, residual CPO activity
F310L
-
is slightly yellow, the [4Fe-4S] cluster content is slightly reduced, cleaves only one S-adenosylmethionine molecule per molecule protein, no detectable CPO activity
G111V/G113V
-
double mutation of Gly-111 and Gly-113, which are part of the potential GGGTP S-adenosyl-L-methionine binding motif, completely abolishes enzyme activity, reduced Fe-S cluster formation
I329A
Q311A
Y56A
-
appears colorless, the [4Fe-4S] cluster content is slightly reduced, no detectable S-adenosylmethionine cleavage, no detectable CPO activity
Y56F
-
mutant with 45% of wild-type activity and reduced Fe-S cluster formation
Y56L
-
appears colorless, the [4Fe-4S] cluster content is slightly reduced, no detectable S-adenosylmethionine cleavage, no detectable CPO activity
Y74F
additional information
I329A
-
contains the same amount of iron-sulfur cluster as the wild-type HemN, but cleaves only one S-adenosylmethionine molecule per molecule protein, no detectable CPO activity
I329A
-
exhibits the same yellow-brown color as wild-type HemN, but the [4Fe-4S] cluster content is slightly reduced and cleaves only one S-adenosylmethionine molecule per molecule protein, no detectable CPO activity
Q311A
-
contains the same amount of iron-sulfur cluster as the wild-type HemN, but cleaves only one S-adenosylmethionine molecule per molecule protein, no detectable CPO activity
Q311A
-
exhibits the same yellow-brown color as wild-type HemN, but the [4Fe-4S] cluster content is slightly reduced and cleaves only one S-adenosylmethionine molecule per molecule protein, no detectable CPO activity
Y74F
-
the apparent binding affinity of the mutant enzyme for the cofactor S-adenosyl-L-methionine is higher than that of the wild type enzyme
Y74F
-
the apparent binding affinity of the mutant enzyme for the cofactor S-adenosyl-L-methionine is higher than that of the wild type enzyme
-
additional information
enzyme knockout by T-DNA insertions in the HEMN1 gene. A 17fold downregulation of AtHEMN1 transcripts occurs in the mutant. The plastidial CPO gene (LIN2) also shows 3.7fold downregulation. The AtHEMN1 mutation prevents the fusion of polar nuclei in the female gametophyte and affects endosperm proliferation. Phenotype, overview
additional information
-
enzyme knockout by T-DNA insertions in the HEMN1 gene. A 17fold downregulation of AtHEMN1 transcripts occurs in the mutant. The plastidial CPO gene (LIN2) also shows 3.7fold downregulation. The AtHEMN1 mutation prevents the fusion of polar nuclei in the female gametophyte and affects endosperm proliferation. Phenotype, overview
additional information
-
construction of deletion mutants of the HemN genes, growth of the mutant DELTAsll1876 is significantly slower than that of the wild-type under microoxic conditions, while it grows normally under aerobic conditions. Coproporphyrin III is accumulated at a low but significant level in the DELTAsll1876 mutant grown under micro-oxic conditions. No detectable phenotype in DELTAsll1917 under the conditions, phenotypes, overview
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant GST-tagged enzyme by glutathione affinity chromatography and ultrafiltration
-
recombinant His-tagged full-length enzyme and viperin (214-361) from Escherichia coli strain BL21 inclusion bodies, solubilization by 8 M urea and purification by nickel affinity chromatography and gel filtration
-
recombinant His-tagged HemN from Escherichia coli strain BL21(DE3) membranes by nickel affinity chromatography and gel filtration
-
recombinant terminally Strep-tagged HemNs from Escherichia coli to homogeneity
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene cig5, expression of viperin lacking the leucine zipper domain, viperin43-340, in Escherichia coli Rosetta(DE3)pLysS cells
-
gene HEMN1, promoter and transcript analyses of AtHEMN1, recombinant expression of AtHEMN1-GFP fusion protein in mitochondria, quantitative reverse transcription PCR enzyme expression analysis
gene hemW or hemN, recombinant expression in the hemN-deficient Escherichia coli mutant strain JW3838 and in strain BL21(DE3) as His-tagged protein. Lactococcus lactis HemW at high levels does not complement the growth deficit of the Escherichia coli DELTAhemN mutant
-
genes sll1876 and sll1917, overexpression of N-terminally Strep-tagged HemNs in Escherichia coli
-
viperin from monocytic cells, DNA and amino acid sequence determination and analysis, expression of His-tagged full-length enzyme, and of His-tagged viperin (45-361) and viperin (214-361) in Escherichia coli strain BL21
-
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
HemN expression or activity is affected in the copA- mutant under excess copper
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
recombinant soluble His-tagged viperin (45-361) from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, recombinant His-tagged full-length enzyme and viperin (214-361) from Escherichia coli strain BL21 inclusion bodies is solubilized by 8 M urea and further renaturated and purificated by nickel affinity chromatography and gel filtration. Reconstitution of the [4Fe-4S] cluster in Viperin residues 45-361, overview
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pharmacology
the structure of HemN sets the stage for the development of inhibitors with antibacterial function due to the uniquely bacterial occurence of the enzyme
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Layer, G.; Moser, J.; Heinz, D.W.; Jahn, D.; Schubert, W.D.
Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes
EMBO J.
22
6214-6224
2003
Escherichia coli (P32131), Escherichia coli
brenda
Layer, G.; Verfurth, K.; Mahlitz, E.; Jahn, D.
Oxygen-independent coproporphyrinogen-III oxidase HemN from Escherichia coli
J. Biol. Chem.
277
34136-34142
2002
Escherichia coli
brenda
Layer, G.; Heinz, D.W.; Jahn, D.; Schubert, W.D.
Structure and function of radical SAM enzymes
Curr. Opin. Chem. Biol.
8
468-476
2004
Escherichia coli
brenda
Layer, G.; Kervio, E.; Morlock, G.; Heinz, D.W.; Jahn, D.; Retey, J.; Schubert, W.D.
Structural and functional comparison of HemN to other radical SAM enzymes
Biol. Chem.
386
971-980
2005
Bacillus subtilis, Cereibacter sphaeroides, Cupriavidus necator, Escherichia coli, Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Layer, G.; Grage, K.; Teschner, T.; Schuenemann, V.; Breckau, D.; Masoumi, A.; Jahn, M.; Heathcote, P.; Trautwein, A.X.; Jahn, D.
Radical S-adenosylmethionine enzyme coproporphyrinogen III oxidase HemN: functional features of the [4Fe-4S] cluster and the two bound S-adenosyl-L-methionines
J. Biol. Chem.
280
29038-29046
2005
Escherichia coli
brenda
Layer, G.; Pierik, A.J.; Trost, M.; Rigby, S.E.; Leech, H.K.; Grage, K.; Breckau, D.; Astner, I.; Jaensch, L.; Heathcote, P.; Warren, M.J.; Heinz, D.W.; Jahn, D.
The substrate radical of Escherichia coli oxygen-independent coproporphyrinogen III oxidase HemN
J. Biol. Chem.
281
15727-15734
2006
Escherichia coli
brenda
Yokoyama, K.; Ohmori, D.; Kudo, F.; Eguchi, T.
Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy
Biochemistry
47
8950-8960
2008
Niallia circulans
brenda
Frey, P.A.; Hegeman, A.D.; Ruzicka, F.J.
The radical SAM superfamily
Crit. Rev. Biochem. Mol. Biol.
43
63-88
2008
Homo sapiens
brenda
Yokoyama, K.; Numakura, M.; Kudo, F.; Ohmori, D.; Eguchi, T.
Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin
J. Am. Chem. Soc.
129
15147-15155
2007
Niallia circulans
brenda
Shaveta, G.; Shi, J.; Chow, V.T.; Song, J.
Structural characterization reveals that viperin is a radical S-adenosyl-L-methionine (SAM) enzyme
Biochem. Biophys. Res. Commun.
391
1390-1395
2010
Homo sapiens
brenda
Rand, K.; Noll, C.; Schiebel, H.M.; Kemken, D.; Duelcks, T.; Kalesse, M.; Heinz, D.W.; Layer, G.
The oxygen-independent coproporphyrinogen III oxidase HemN utilizes harderoporphyrinogen as a reaction intermediate during conversion of coproporphyrinogen III to protoporphyrinogen IX
Biol. Chem.
391
55-63
2010
Escherichia coli
brenda
Duschene, K.S.; Broderick, J.B.
The antiviral protein viperin is a radical SAM enzyme
FEBS Lett.
584
1263-1267
2010
Homo sapiens
brenda
Goto, T.; Aoki, R.; Minamizaki, K.; Fujita, Y.
Functional differentiation of two analogous coproporphyrinogen III oxidases for heme and chlorophyll biosynthesis pathways in the cyanobacterium Synechocystis sp. PCC 6803
Plant Cell Physiol.
51
650-663
2010
Synechocystis sp.
brenda
Abicht, H.K.; Martinez, J.; Layer, G.; Jahn, D.; Solioz, M.
Lactococcus lactis HemW (HemN) is a haem-binding protein with a putative role in haem trafficking
Biochem. J.
442
335-343
2012
Lactococcus lactis
brenda
Azzouzi, A.; Steunou, A.S.; Durand, A.; Khalfaoui-Hassani, B.; Bourbon, M.L.; Astier, C.; Bollivar, D.W.; Ouchane, S.
Coproporphyrin III excretion identifies the anaerobic coproporphyrinogen III oxidase HemN as a copper target in the Cu+-ATPase mutant copA- of Rubrivivax gelatinosus
Mol. Microbiol.
88
339-351
2013
Rubrivivax gelatinosus (I0HU37), Rubrivivax gelatinosus
brenda
Kim, E.J.; Oh, E.K.; Lee, J.K.
Role of HemF and HemN in the heme biosynthesis of Vibrio vulnificus under S-adenosylmethionine-limiting conditions
Mol. Microbiol.
96
497-512
2015
Vibrio vulnificus, Vibrio vulnificus ATCC 29307
brenda
Azzouzi, A.; Steunou, A.S.; Durand, A.; Khalfaoui-Hassani, B.; Bourbon, M.L.; Astier, C.; Bollivar, D.W.; Ouchane, S.
Coproporphyrin III excretion identifies the anaerobic coproporphyrinogen III oxidase HemN as a copper target in the Cu+-ATPase mutant copA- of Rubrivivax gelatinosus
Mol. Microbiol.
88
339-351
2013
Rubrivivax gelatinosus (I0HU37), Rubrivivax gelatinosus
brenda
Pratibha, P.; Singh, S.K.; Srinivasan, R.; Bhat, S.R.; Sreenivasulu, Y.
Gametophyte development needs mitochondrial coproporphyrinogen III oxidase function
Plant Physiol.
174
258-275
2017
Arabidopsis thaliana (Q9FMJ4), Arabidopsis thaliana
brenda
Ji, X.; Mo, T.; Liu, W.Q.; Ding, W.; Deng, Z.; Zhang, Q.
Revisiting the mechanism of the anaerobic coproporphyrinogen III oxidase HemN
Angew. Chem. Int. Ed. Engl.
58
6235-6238
2019
Escherichia coli
brenda
Choby, J.E.; Skaar, E.P.
Staphylococcus aureus Coproporphyrinogen III Oxidase is required for aerobic and anaerobic heme synthesis
mSphere
4
e00235-19
2019
Staphylococcus aureus
brenda
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