Information on EC 1.97.1.4 - [formate-C-acetyltransferase]-activating enzyme

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY
1.97.1.4
-
RECOMMENDED NAME
GeneOntology No.
[formate-C-acetyltransferase]-activating enzyme
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical
show the reaction diagram
the glycyl radical in pyruvate formate-lyase is produced by stereospecific abstraction of the pro-S hydrogen of Gly734 by the 5'-deoxyadenosine radical generated in the active center of the enzyme
-
S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical
show the reaction diagram
mechanism, a deoxyadenosyl radical intermediate, generated by the reductive cleavage of S-adenosylmethionine serves as the actual H atom abstracting species
-
S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical
show the reaction diagram
4Fe-4S cluster is involved in catalysis by coordinating S-adenosyl-L-methionine
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
oxidation
-
-
-
-
reduction
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
[formate C-acetyltransferase]-glycine dihydroflavodoxin:S-adenosyl-L-methionine oxidoreductase (S-adenosyl-L-methionine cleaving)
An iron-sulfur protein. A single glycine residue in EC 2.3.1.54, formate C-acetyltransferase, is oxidized to the corresponding radical by transfer of H from its CH2 to AdoMet with concomitant cleavage of the latter. The reaction requires Fe2+. The first stage is reduction of the AdoMet to give methionine and the 5'-deoxyadenosin-5'-yl radical, which then abstracts a hydrogen radical from the glycine residue.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Activase, pyruvate formate-lyase
-
-
-
-
Formate acetyltransferase activase
-
-
-
-
Formate-lyase-activating enzyme
-
-
-
-
PFL
P0A9N4
-
PFL activase
-
-
-
-
PFL activating enzyme
Q6RFH6
-
PFL-activating enzyme
-
-
-
-
PFL-AE
-
-
-
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PFL-glycine:S-adenosyl-L-methionine H transferase (flavodoxin-oxidizing, S-adenosyl-L-methionine-cleaving)
-
-
-
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pyruvate formate lyase activating enzyme
Q6RFH6
-
Pyruvate formate-lyase activase
-
-
-
-
Pyruvate formate-lyase activating enzyme
-
-
-
-
pyruvate formate-lyase-activating enzyme
-
-
CAS REGISTRY NUMBER
COMMENTARY
206367-15-9
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
induction of transcription by anaerobiosis and darkness, but little induction on protein level
-
-
Manually annotated by BRENDA team
strain 27405. Enzyme activity is present in late log and stationary growth phase of cells grown on cellobiose
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-
Manually annotated by BRENDA team
Ruminiclostridium thermocellum 27405.
strain 27405. Enzyme activity is present in late log and stationary growth phase of cells grown on cellobiose
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
metabolism
P0A9N4
enzyme is activated by pyruvate formate-lyase-activating enzyme by generating a catalytically essential radical on residue Gly734. In the open conformation of the enzyme, the Gly734 residue is located not in its buried position in the enzyme active site but rather in a more solvent-exposed location. The presence of the activating enzyme increases the proportion of enzyme in the open conformation. The activating enzyme accesses residue Gly734 for direct hydrogen atom abstraction by binding to the Gly734 loop in the open conformation, thereby shifting the closed open equilibrium of the enzyme to the right
physiological function
P0A9N4
pyruvate formate-lyase-activating enzyme (PFL-AE) activates pyruvate formate-lyase
physiological function
-
holo-flavodoxin is capable of associating with NADP+-dependent flavodoxin oxidoreductase and pyruvate formate-lyase activating enzyme, whereas there is no detectable interaction between apo-flavodoxin. Holo-flavodoxin interacts with pyruvate formate-lyase activating enzyme with a dissociation constant of 23.3 microM
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
-
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
-
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
-
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
-
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
-
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
-
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
-
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
-
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
formate acetyltransferase-glycine is the inactive form of the enzyme
formate acetyltransferase-glycine-2-yl-radical is the active form of the enzyme
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
the glycyl radical in pyruvate formate-lyase is produced by stereospecific abstraction of the pro-S hydrogen of Gly734 by the 5'-deoxyadenosine radical generated in the active center of the enzyme
-
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
the interaction with substrate formate C-acetyltransferase is very slow and rate-limited by large conformational changes. The enzyme binds S-adenosyl-L-methionine with the same affinity of about 0.006 mM regardless of the presence or absence of formate C-acetyltransferase. Activation of formate C-acetyltransferase in the presence of its substrate pyruvate or the analogue oxamate results in stoichiometric conversion of the [4Fe-4S]1+ cluster to the glycyl radical on formate C-acetyltransferase, however 3.7-fold less activation is achieved in the absence of these small molecules. Formate C-acetyltransferase, formate C-acetyltransferase activating enzyme, and S-adenosyl-L-methionine are essentially fully bound in vivo, whereas electron donor proteins are partially bound
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-
?
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
Clostridium pasteurianum DSM525
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-
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S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
Escherichia coli K12
-
formate acetyltransferase-glycine is the inactive form of the enzyme
formate acetyltransferase-glycine-2-yl-radical is the active form of the enzyme
-
S-adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + flavodoxin + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
Escherichia coli K12
-
-
-
-
S-Adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
?
show the reaction diagram
-
-
-
-
-
S-adenosyl-L-methionine + NADH + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + NAD+ + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
40% of activity with reduced methyl viologen
-
?
S-adenosyl-L-methionine + NADPH + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + NADP+ + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
95% of activity with reduced methyl viologen
-
-
?
S-adenosyl-L-methionine + reduced methyl viologen + formate acetyltransferase-glycine
5'-deoxyadenosine + methionine + methyl viologen + formate acetyltransferase-glycine-2-yl-radical
show the reaction diagram
-
-
-
-
?
additional information
?
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the enzyme also activates an enzyme which has both pyruvate formate-lyase activity and 2-ketobutyrate formate-lyase activity
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additional information
?
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a DELTAAla-containing peptide which lacks hydrogens at the 734-Calpha atom is recognized by the enzyme and is able to trap covalently the nucleophilic 5-deoxyadenosine radical
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additional information
?
-
P0A9N4
pyruvate formate-lyase-activating enzyme (PFL-AE) activates pyruvate formate-lyase by generating a catalytically essential radical on Gly-734 of pyruvate formate-lyase. PFL-AE shifts the closed/open formation of pyruvate formate-lyase to the open conformation, in which Gly-734 is more solvent-exposed and accessible to the PFL-AE active site
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
S-Adenosyl-L-methionine + dihydroflavodoxin + formate acetyltransferase-glycine
?
show the reaction diagram
-
-
-
-
-
additional information
?
-
P0A9N4
pyruvate formate-lyase-activating enzyme (PFL-AE) activates pyruvate formate-lyase by generating a catalytically essential radical on Gly-734 of pyruvate formate-lyase. PFL-AE shifts the closed/open formation of pyruvate formate-lyase to the open conformation, in which Gly-734 is more solvent-exposed and accessible to the PFL-AE active site
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COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
S-adenosyl-L-methionine
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[4Fe-4S]-center
-
an increase in pre-edge intensity is due to additional contributions from sulfide and thiolate of the Fe4S4 cluster into the C-S sigma* orbital. There is a backbonding interaction between the Fe4S4 cluster and C-S sigma* orbitals of S-adenosyl-L-methionine in this inner sphere complex. This backbonding is enhanced in the reduced form and this configurational interaction between the donor and acceptor orbitals facilitates the electron transfer from the cluster to S-adenosyl-L-methionine, that otherwise has a large outer sphere electron transfer barrier. The energy of the reductive cleavage of the C-S bond is sensitive to the dielectric of the protein in the immediate vicinity of the site as a high dielectric stabilizes the more charge separated reactant increasing the reaction barrier
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Cobalt
-
Co(II) and Cu(II) can be reconstituted into the protein with similar stoichiometry
copper
-
Co(II) and Cu(II) can be reconstituted into the protein with similar stoichiometry
Fe2+
Q93UQ7, -
required
Iron
-
[4Fe-4S]2+clusters at the subunit interface can undergoe reversible oxidative conversion to [2Fe-2S]2+clusters under conditions of incomplete anaerobicity
Iron
-
contains an iron-sulfur cluster, most probably of the [4Fe-4S]type
Iron
-
binds one Fe(II) per protein monomer. Co(II) and Cu(II) can be reconstituted into the protein with similar stoichiometry
Iron
-
2.8 mol per mol of enzyme, as (3Fe-4S)+ cluster
Iron
-
anaerobically purified enzyme, 4FE-4S cluster in a diamagnetic 2+ oxidation state
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
peptides
-
peptides homologous to the Gly734 site of pyruvate formate-lyase that are active as substrates
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
additional information
-
contains a covalently bound chromophoric factor which has an optical absorptiion peak at 388 nm
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0012
-
inactive pyruvate formate-lyase
-
-
-
0.0028
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S-adenosyl-L-methionine
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SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.017
-
-
-
43
-
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25°C, pH 8.1
105
-
-
pH 6.8, 30°C
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.7
-
-
20% of activity at pH 6.8
pI VALUE
pI VALUE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.8
-
-
isoelectric focusing
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
28000
-
-
gel filtration
30000
-
Q93UQ7, -
gel filtration
34000
-
-
gel filtration
40000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 28035, calculation from nucleotide sequence
?
Escherichia coli K12
-
x * 28035, calculation from nucleotide sequence
-
dimer
-
2 * 28000
monomer
-
1 * 29500, SDS-PAGE
monomer
Q93UQ7, -
1 * 29900, calculated, 1 * 30000, SDS-PAGE
monomer
Escherichia coli K12
-
1 * 29500, SDS-PAGE
-
additional information
P0A9N4
model in which the enzyme can exist in either a closed conformation, with residue Gly734 buried in the active site and harboring a stable glycyl radical, or an open conformation, with Gly734 more solvent-exposed and accessible to the activating enzyme's active site
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
modeling of the complex between pyruvate formate-lyase activating enzyme and flavodoxin. In the pyruvate formate-lyase activating enzyme/flavodoxin complex, FMN is located 10.7 A from the [4Fe-4S] cluster in pyruvate formate-lyase activating enzyme. The flavodoxin binding site on pyruvate formate-lyase activating enzyme is the only location other than the pyruvate formate-lyase binding site where the [4Fe-4S] cluster is close to the surface of the enzyme, which would be necessary for efficient electron transfer
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
4°C, presence of Fe(SO4)2(NH4)2 and dithiothreitol, relatively stable
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
using strictly anaerobic conditions
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
clone encodes a putative protein of 8532 amino acids
-
over-expressed in Escherichia coli
P0A9N4
overexpression in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
C102S
-
mutant enzymes C12S, C94S, C102S display full holoactivase activity, albeit absolute values are slightly lower, by a factor of 2 than the value of the wild type enzyme. Mutant enzymes C29S, C33S and C36S are catalytically incompetent
C12S
-
mutant enzymes C12S, C94S, C102S display full holoactivase activity, albeit absolute values are slightly lower, by a factor of 2 than the value of the wild type enzyme. Mutant enzymes C29S, C33S and C36S are catalytically incompetent
C29S
-
mutant enzymes C12S, C94S, C102S display full holoactivase activity, albeit absolute values are slightly lower, by a factor of 2 than the value of the wild type enzyme. Mutant enzymes C29S, C33S and C36S are catalytically incompetent
C33S
-
mutant enzymes C12S, C94S, C102S display full holoactivase activity, albeit absolute values are slightly lower, by a factor of 2 than the value of the wild type enzyme. Mutant enzymes C29S, C33S and C36S are catalytically incompetent
C36S
-
mutant enzymes C12S, C94S, C102S display full holoactivase activity, albeit absolute values are slightly lower, by a factor of 2 than the value of the wild type enzyme. Mutant enzymes C29S, C33S and C36S are catalytically incompetent
C94S
-
mutant enzymes C12S, C94S, C102S display full holoactivase activity, albeit absolute values are slightly lower, by a factor of 2 than the value of the wild type enzyme. Mutant enzymes C29S, C33S and C36S are catalytically incompetent
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
medicine
-
in dental plaque, under anaerobic conditions, enzyme is always kept active