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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 enzyme appears in viruses and cellular organisms
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