BRENDA - Enzyme Database show
show all sequences of 1.3.98.3

Structure and function of radical SAM enzymes

Layer, G.; Heinz, D.W.; Jahn, D.; Schubert, W.D.; Curr. Opin. Chem. Biol. 8, 468-476 (2004)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
crystal structure
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
coproporphyrinogen-III + S-adenosyl-L-methionine
Escherichia coli
HemN catalyzes the prepenultimate step in anaerobic heme biosynthesis
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
-
-
-
Reaction
Reaction
Commentary
Organism
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 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. The conversion of –.CH-CH2-COO- leading to –CH=CH2 + CO2 + e- replaces the electron initially used, reaction mechanism
Escherichia coli
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
coproporphyrinogen-III + S-adenosyl-L-methionine
HemN catalyzes the prepenultimate step in anaerobic heme biosynthesis
658501
Escherichia coli
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
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
658501
Escherichia coli
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
?
Subunits
Subunits
Commentary
Organism
monomer
-
Escherichia coli
Cofactor
Cofactor
Commentary
Organism
Structure
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
Escherichia coli
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
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
Escherichia coli
Crystallization (Commentary) (protein specific)
Crystallization
Organism
crystal structure
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
coproporphyrinogen-III + S-adenosyl-L-methionine
Escherichia coli
HemN catalyzes the prepenultimate step in anaerobic heme biosynthesis
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
coproporphyrinogen-III + S-adenosyl-L-methionine
HemN catalyzes the prepenultimate step in anaerobic heme biosynthesis
658501
Escherichia coli
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
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
658501
Escherichia coli
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
monomer
-
Escherichia coli
Other publictions for EC 1.3.98.3
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)
746121
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739104
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Role of HemF and HemN in the h ...
Vibrio vulnificus, Vibrio vulnificus ATCC 29307
Mol. Microbiol.
96
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726009
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745799
Azzouzi
Coproporphyrin III excretion ...
Rubrivivax gelatinosus
Mol. Microbiol.
88
339-351
2013
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724235
Abicht
Lactococcus lactis HemW (HemN) ...
Lactococcus lactis
Biochem. J.
442
335-343
2012
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711084
Shaveta
Structural characterization re ...
Homo sapiens
Biochem. Biophys. Res. Commun.
391
1390-1395
2010
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711348
Rand
The oxygen-independent copropo ...
Escherichia coli
Biol. Chem.
391
55-63
2010
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712016
Duschene
The antiviral protein viperin ...
Homo sapiens
FEBS Lett.
584
1263-1267
2010
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713258
Goto
Functional differentiation of ...
Synechocystis sp.
Plant Cell Physiol.
51
650-663
2010
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685280
Yokoyama
Mechanistic study on the react ...
Bacillus circulans
Biochemistry
47
8950-8960
2008
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686237
Frey
The radical SAM superfamily ...
Homo sapiens
Crit. Rev. Biochem. Mol. Biol.
43
63-88
2008
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687282
Yokoyama
Characterization and mechanist ...
Bacillus circulans
J. Am. Chem. Soc.
129
15147-15155
2007
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674567
Layer
The substrate radical of Esche ...
Escherichia coli
J. Biol. Chem.
281
15727-15734
2006
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672473
Layer
Structural and functional comp ...
Bacillus subtilis, Cupriavidus necator, Escherichia coli, Rhodobacter sphaeroides, Salmonella enterica subsp. enterica serovar Typhimurium
Biol. Chem.
386
971-980
2005
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674462
Layer
Radical S-adenosylmethionine e ...
Escherichia coli
J. Biol. Chem.
280
29038-29046
2005
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658501
Layer
Structure and function of radi ...
Escherichia coli
Curr. Opin. Chem. Biol.
8
468-476
2004
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655340
Layer
Crystal structure of coproporp ...
Escherichia coli
EMBO J.
22
6214-6224
2003
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656073
Layer
Oxygen-independent coproporphy ...
Escherichia coli
J. Biol. Chem.
277
34136-34142
2002
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