BRENDA - Enzyme Database show
show all sequences of 1.3.98.3

Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes

Layer, G.; Moser, J.; Heinz, D.W.; Jahn, D.; Schubert, W.D.; EMBO J. 22, 6214-6224 (2003)

Data extracted from this reference:

Application
Application
Commentary
Organism
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
Escherichia coli
Cloned(Commentary)
Commentary
Organism
-
Escherichia coli
Crystallization (Commentary)
Crystallization
Organism
crystal structure, co-crystallized with S-adenosyl-L-methionine, hanging-drop vapor diffusion method, X-ray analysis
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 essential conversion of coproporphyrinogen-III to protoporphyrinogen IX during heme biosynthesis
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
P32131
-
-
Purification (Commentary)
Commentary
Organism
recombinant HemN
Escherichia coli
Reaction
Reaction
Commentary
Organism
coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine
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 essential conversion of coproporphyrinogen-III to protoporphyrinogen IX during heme biosynthesis
655340
Escherichia coli
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
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
655340
Escherichia coli
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
?
Subunits
Subunits
Commentary
Organism
monomer
monomeric enzyme consisting of two distinct domains
Escherichia coli
Cofactor
Cofactor
Commentary
Organism
Structure
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
Escherichia coli
S-adenosyl-L-methionine
HemN contains two S-adenosyl-L-methionine molecules as cofactors, detailed binding mode
Escherichia coli
Application (protein specific)
Application
Commentary
Organism
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
Escherichia coli
Cloned(Commentary) (protein specific)
Commentary
Organism
-
Escherichia coli
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
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
Escherichia coli
S-adenosyl-L-methionine
HemN contains two S-adenosyl-L-methionine molecules as cofactors, detailed binding mode
Escherichia coli
Crystallization (Commentary) (protein specific)
Crystallization
Organism
crystal structure, co-crystallized with S-adenosyl-L-methionine, hanging-drop vapor diffusion method, X-ray analysis
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 essential conversion of coproporphyrinogen-III to protoporphyrinogen IX during heme biosynthesis
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant HemN
Escherichia coli
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 essential conversion of coproporphyrinogen-III to protoporphyrinogen IX during heme biosynthesis
655340
Escherichia coli
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
?
coproporphyrinogen-III + S-adenosyl-L-methionine
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
655340
Escherichia coli
protoporphyrinogen IX + CO2 + L-methionine + 5'-deoxyadenosine
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
monomer
monomeric enzyme consisting of two distinct domains
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)
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739104
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Coproporphyrin III excretion i ...
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Azzouzi
Coproporphyrin III excretion ...
Rubrivivax gelatinosus
Mol. Microbiol.
88
339-351
2013
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724235
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Lactococcus lactis
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Structural characterization re ...
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Functional differentiation of ...
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Yokoyama
Characterization and mechanist ...
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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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Layer
Radical S-adenosylmethionine e ...
Escherichia coli
J. Biol. Chem.
280
29038-29046
2005
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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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