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Information on EC 4.3.99.4 - choline trimethylamine-lyase
for references in articles please use BRENDA:EC4.3.99.4
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EC Tree 4 Lyases
4.3 Carbon-nitrogen lyases
4.3.99 Other carbon-nitrogen lyases
4.3.99.4 choline trimethylamine-lyase
IUBMB Comments
The enzyme utilizes a glycine radical to break the C-N bond in choline. Found in choline-degrading anaerobic bacteria.
The expected taxonomic range for this enzyme is: Bacteria, Archaea
- 4.3.99.4
- toluene
- p-cresol
- formate-lyase
-
thiyl
- 4-hydroxyphenylacetate
- aromatica
- thauera
-
r-benzylsuccinate
-
radical-based
showSynonyms
glycyl radical enzyme, choline tma-lyase, choline trimethylamine-lyase, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
choline TMA-lyase
cutC
Dde_3282
glycyl radical enzyme
glycyl radical enzyme
Oleidesulfovibrio alaskensis G20
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
choline = trimethylamine + acetaldehyde
-
-
-
-
choline = trimethylamine + acetaldehyde
radical reaction or rearrangement mechanism, overview
Oleidesulfovibrio alaskensis
-
choline = trimethylamine + acetaldehyde
radical reaction or rearrangement mechanism, overview
Oleidesulfovibrio alaskensis G20
-
-
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SYSTEMATIC NAME
IUBMB Comments
choline trimethylamine-lyase (acetaldehyde-forming)
The enzyme utilizes a glycine radical to break the C-N bond in choline. Found in choline-degrading anaerobic bacteria.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
choline
trimethylamine + acetaldehyde
Substrates: -
Products: a glycyl radical-based mechanism of C-N cleavage
Products: a glycyl radical-based mechanism of C-N cleavage
?
choline
trimethylamine + acetaldehyde
Substrates: -
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis
-
Substrates: -
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis
Substrates: -
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis
Substrates: -
Products: a glycyl radical-based mechanism of C-N cleavage
Products: a glycyl radical-based mechanism of C-N cleavage
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis
-
Substrates: the enzyme shows strict specificity for choline
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis
Substrates: important route for the production of trimethylamine
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis G20
-
Substrates: -
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis G20
-
Substrates: the enzyme shows strict specificity for choline
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis G20
Substrates: -
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis G20
Substrates: important route for the production of trimethylamine
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis G20
Substrates: -
Products: a glycyl radical-based mechanism of C-N cleavage
Products: a glycyl radical-based mechanism of C-N cleavage
?
additional information
?
-
Oleidesulfovibrio alaskensis
-
Substrates: the enzyme CutC is a C-N bond-cleaving glycyl radical enzyme
Products: -
Products: -
?
additional information
?
-
Oleidesulfovibrio alaskensis G20
-
Substrates: the enzyme CutC is a C-N bond-cleaving glycyl radical enzyme
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis
-
Substrates: -
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis
Substrates: important route for the production of trimethylamine
Products: -
Products: -
?
choline
trimethylamine + acetaldehyde
Oleidesulfovibrio alaskensis G20
-
Substrates: -
Products: -
Products: -
?
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
GRE activating protein
Oleidesulfovibrio alaskensis
-
i.e. CutD, biochemical function of CutD as a glycyl radical enzyme or CutC activase
-
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Dehydration
Characterization of 1,2-Propanediol Dehydratases Reveals Distinct Mechanisms for B
Heart Diseases
Microbial Transplantation With Human Gut Commensals Containing CutC Is Sufficient to Transmit Enhanced Platelet Reactivity and Thrombosis Potential.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.3025
choline
Oleidesulfovibrio alaskensis
-
recombinant enzyme, pH 8.0, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
747
choline
Oleidesulfovibrio alaskensis
-
calculated from the EPR activation measurement, recombinant enzyme, pH 8.0, temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
22.7
Oleidesulfovibrio alaskensis
-
purified recombinant enzyme, pH 8.0, temperature not specified in the publication
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Oleidesulfovibrio alaskensis
Oleidesulfovibrio alaskensis G20
Oleidesulfovibrio alaskensis
member of the glycyl radical enzyme family
UniProt
brenda
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
additional information
evolution
Oleidesulfovibrio alaskensis
-
choline TMA-lyase belongs to the glycyl radical enzymes (GREs) utilize protein-based radical intermediates to catalyze a variety of reactions, including nucleotide reduction (class III ribonucleotide reductase (RNR)), C-C bond formation (benzylsuccinate synthase (BSS)), C-C bond cleavage (pyruvate formate-lyase (PFL) and 4-hydroxyphenylacetate decarboxylase (4-HPAD)), and dehydration (B12-independent glycerol dehydratase (GDH))
evolution
Oleidesulfovibrio alaskensis G20
-
choline TMA-lyase belongs to the glycyl radical enzymes (GREs) utilize protein-based radical intermediates to catalyze a variety of reactions, including nucleotide reduction (class III ribonucleotide reductase (RNR)), C-C bond formation (benzylsuccinate synthase (BSS)), C-C bond cleavage (pyruvate formate-lyase (PFL) and 4-hydroxyphenylacetate decarboxylase (4-HPAD)), and dehydration (B12-independent glycerol dehydratase (GDH))
-
metabolism
Oleidesulfovibrio alaskensis
-
the enzyme is involved in anaerobic choline metabolism and encoded in the choline utilization (cut) gene cluster
metabolism
Oleidesulfovibrio alaskensis G20
-
the enzyme is involved in anaerobic choline metabolism and encoded in the choline utilization (cut) gene cluster
-
physiological function
Oleidesulfovibrio alaskensis
gene disruption impairs growth on choline and abolishes production of trimethylamine, with no difference in growth between wild-type and mutant in media containing lactate. Expression of choline trimethylamine-lyase CutC and its activating protein CutD in Escherichia coli BL21 results in production of d9-TMA from (trimethyl-d9)-choline. Expression of either enzyme on its own completely abolishes trimethylamine production
physiological function
Oleidesulfovibrio alaskensis G20
-
gene disruption impairs growth on choline and abolishes production of trimethylamine, with no difference in growth between wild-type and mutant in media containing lactate. Expression of choline trimethylamine-lyase CutC and its activating protein CutD in Escherichia coli BL21 results in production of d9-TMA from (trimethyl-d9)-choline. Expression of either enzyme on its own completely abolishes trimethylamine production
-
additional information
Oleidesulfovibrio alaskensis
-
enzyme homology modeling, docking of choline in the active site of a the enzyme, docking model, overview
additional information
Oleidesulfovibrio alaskensis G20
-
enzyme homology modeling, docking of choline in the active site of a the enzyme, docking model, overview
-
Show AA Sequence and Transmembrane Helices (684 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
124000
mass spectrometry analysis. The 124-kDa full-length CutC protein is very unstable, with the N-terminal part starting to degrade almost immediately after purification by nickel affinity chromatography
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
homodimer
Oleidesulfovibrio alaskensis
-
dimeric oligomerization state for full-length CutC and all of the variants
homodimer
Oleidesulfovibrio alaskensis G20
-
dimeric oligomerization state for full-length CutC and all of the variants
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting drop method, crystal structures of both the choline-bound and choline free forms of CutC are determined, binding of choline at the ligand-binding site triggers conformational changes in the enzyme structure. Choline-bound CutC crystals exhibit an orthorhombic lattice and space group P212121 with 8 molecules in the asymmetric unit. CutC crystals without choline exhibited a monoclinic lattice and space group P21 with 4 molecules in the asymmetric unit
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
T502A
Oleidesulfovibrio alaskensis
turnover number for choline is 4400fold lower than for wild-type enzyme
Y208F
Oleidesulfovibrio alaskensis
turnover number for choline is 215fold lower than for wild-type enzyme
Y208F/Y506F
Oleidesulfovibrio alaskensis
turnover number for choline is 1050fold lower than for wild-type enzyme
Y506F
Oleidesulfovibrio alaskensis
turnover number for choline is 48fold lower than for wild-type enzyme
C489A
Oleidesulfovibrio alaskensis G20
-
complete loss of activity
-
E491A
Oleidesulfovibrio alaskensis G20
-
no activity detectable
-
E491Q
Oleidesulfovibrio alaskensis G20
-
no activity detectable
-
G821A
Oleidesulfovibrio alaskensis G20
-
complete loss of activity
-
T334S
Oleidesulfovibrio alaskensis G20
-
site-directed mutagenesis, the mutant retains activity
-
T502A
Oleidesulfovibrio alaskensis G20
-
turnover number for choline is 4400fold lower than for wild-type enzyme
-
T502S
Oleidesulfovibrio alaskensis G20
-
site-directed mutagenesis, the mutant retains activity
-
Y208F
Oleidesulfovibrio alaskensis G20
-
turnover number for choline is 215fold lower than for wild-type enzyme
-
Y506F
Oleidesulfovibrio alaskensis G20
-
turnover number for choline is 48fold lower than for wild-type enzyme
-
additional information
additional information
Oleidesulfovibrio alaskensis
-
condtruction of a -52 amino acid truncated variant, removal of the predicted N-terminal microcompartment targeting sequence from CutC improves yields and solubility without impacting activity
additional information
Oleidesulfovibrio alaskensis G20
-
condtruction of a -52 amino acid truncated variant, removal of the predicted N-terminal microcompartment targeting sequence from CutC improves yields and solubility without impacting activity
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant N-terminally His6-tagged wild-type and point and N-terminal truncation mutant enzymes from Escherichia coli
Oleidesulfovibrio alaskensis
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene cutC, cloning and overexpression of the N-terminally His6-tagged wild-type and point and N-terminal truncation mutant enzymes in Escherichia coli
Oleidesulfovibrio alaskensis
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Craciun, S.; Balskus, E.P.
Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme
Proc. Natl. Acad. Sci. USA
109
21307-21312
2012
Desulfovibrio desulfuricans, Desulfovibrio desulfuricans (B8J0I2), Oleidesulfovibrio alaskensis (Q30W70), Oleidesulfovibrio alaskensis G20 (Q30W70)
brenda
Craciun, S.; Marks, J.A.; Balskus, E.P.
Characterization of choline trimethylamine-lyase expands the chemistry of glycyl radical enzymes
ACS Chem. Biol.
9
1408-1413
2014
Oleidesulfovibrio alaskensis, Oleidesulfovibrio alaskensis G20
brenda
Bodea, S.; Funk, M.A.; Balskus, E.P.; Drennan, C.L.
Molecular basis of C-N bond cleavage by the glycyl radical enzyme choline trimethylamine-lyase
Cell Chem. Biol.
23
1206-1216
2016
Oleidesulfovibrio alaskensis (Q30W70), Oleidesulfovibrio alaskensis G20 (Q30W70)
brenda
Kalnins, G.; Kuka, J.; Grinberga, S.; Makrecka-Kuka, M.; Liepinsh, E.; Dambrova, M.; Tars, K.
Structure and function of CutC choline lyase from human microbiota bacterium Klebsiella pneumoniae
J. Biol. Chem.
290
21732-21740
2015
Klebsiella pneumoniae (A0A0M3KL45), Klebsiella pneumoniae
brenda
EXTERNAL LINKS (specific for EC-Number 4.3.99.4)
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Release 2023.1 (January 2023)
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