Information on EC 6.4.1.3 - propionyl-CoA carboxylase

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

EC NUMBER
COMMENTARY hide
6.4.1.3
-
RECOMMENDED NAME
GeneOntology No.
propionyl-CoA carboxylase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + propanoyl-CoA + HCO3- = ADP + phosphate + (S)-methylmalonyl-CoA
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
carboxylation
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
3-hydroxypropanoate cycle
-
-
3-hydroxypropanoate/4-hydroxybutanate cycle
-
-
anaerobic energy metabolism (invertebrates, mitochondrial)
-
-
Biosynthesis of antibiotics
-
-
Carbon fixation pathways in prokaryotes
-
-
CO2 fixation in Crenarchaeota
-
-
Glyoxylate and dicarboxylate metabolism
-
-
Metabolic pathways
-
-
methylaspartate cycle
-
-
Microbial metabolism in diverse environments
-
-
mycolate biosynthesis
-
-
Propanoate metabolism
-
-
propanoyl CoA degradation I
-
-
Valine, leucine and isoleucine degradation
-
-
SYSTEMATIC NAME
IUBMB Comments
propanoyl-CoA:carbon-dioxide ligase (ADP-forming)
A biotinyl-protein. Also carboxylates butanoyl-CoA and catalyses transcarboxylation.
CAS REGISTRY NUMBER
COMMENTARY hide
9023-94-3
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain So4a, DSM 3191
-
-
Manually annotated by BRENDA team
strain So4a, DSM 3191
-
-
Manually annotated by BRENDA team
IAM13299
-
-
Manually annotated by BRENDA team
IAM13299
-
-
Manually annotated by BRENDA team
ORS571
-
-
Manually annotated by BRENDA team
ORS571
-
-
Manually annotated by BRENDA team
USDA110
-
-
Manually annotated by BRENDA team
USDA110
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain OK-70-fl, DSM 636
-
-
Manually annotated by BRENDA team
strain OK70-fl, DSM 636
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
I3R7G3: biotin carboxylase subunit (PccA), I3R7F1: carboxyltransferase component (PccB), I3R7F2: essential small subunit PccX
I3R7G3 and I3R7F1 and I3R7F2
UniProt
Manually annotated by BRENDA team
CCBAU2609
-
-
Manually annotated by BRENDA team
CCBAU2609
-
-
Manually annotated by BRENDA team
NZP2037
-
-
Manually annotated by BRENDA team
NZP2037
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
propionate- or valine-grown
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
MNF300
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
USDA205
-
-
Manually annotated by BRENDA team
USDA205
-
-
Manually annotated by BRENDA team
Rm1021
-
-
Manually annotated by BRENDA team
Rm1021
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain Kra23, DSM 6482
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
I3R7G3 and I3R7F1 and I3R7F2
gene knockout/complementation demonstrates that the enzyme consists of a fusion protein of a biotin carboxylase and a biotin-carboxyl carrier protein (PccA, HFX_2490), a carboxyltransferase component (PccB, HFX_2478), and an essential small subunit (PccX, HFX_2479). Knockout of pccBX leads to an inability to utilize propionate and a higher intracellular propionyl-CoA level, indicating that the enzyme is indispensable for propionyl-CoA utilization. the pccBX-deleted strain displays multiple phenotypic changes, including retarded cell growth, decreased glucose consumption, impaired PHBV biosynthesis, and wrinkled cells. Genome-wide microarray analysis shows that many genes for glycolysis, pyruvate oxidation, PHBV accumulation, electron transport, and stress responses are affected in the pccBX-deleted strain
metabolism
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
acetyl-CoA + CO2
?
show the reaction diagram
ATP + acetyl-CoA + HCO3-
?
show the reaction diagram
Q877I4 and Q877I3 and Q877I5
n-butyryl-CoA (0.5 mM) is carboxylated at 4.6% compared to carboxylation of acetyl-CoA or propionyl-CoA
-
-
?
ATP + acetyl-CoA + HCO3-
ADP + phosphate + malonyl-CoA
show the reaction diagram
ATP + butanoyl-CoA + HCO3-
ADP + phosphate + ?
show the reaction diagram
ATP + butyryl-CoA + HCO3-
ADP + phosphate + ?
show the reaction diagram
-
-
-
?
ATP + crotonyl-CoA + HCO3-
ADP + phosphate + ?
show the reaction diagram
-
at 3% the velocity compared to propanoyl-CoA
-
-
-
ATP + propanoyl-CoA + HCO3-
?
show the reaction diagram
-
key enzyme of the 3-hydroxypropanoate cycle
-
-
-
ATP + propanoyl-CoA + HCO3-
ADP + phosphate + (2S)-methylmalonyl-CoA
show the reaction diagram
-
-
-
-
?
ATP + propanoyl-CoA + HCO3-
ADP + phosphate + (S)-methylmalonyl-CoA
show the reaction diagram
ATP + propanoyl-CoA + HCO3-
ADP + phosphate + methylmalonyl-CoA
show the reaction diagram
ATP + propionyl-CoA + HCO3-
ADP + phosphate + (S)-methylmalonyl-CoA
show the reaction diagram
-
preferred substrate
-
-
?
ATP + succinyl-CoA + HCO3-
ADP + phosphate + ?
show the reaction diagram
-
-
-
?
butyryl-CoA + CO2
?
show the reaction diagram
-
-
-
?
GTP + propanoyl-CoA + HCO3-
GDP + phosphate + (S)-methylmalonyl-CoA
show the reaction diagram
propionyl-CoA + CO2
(2S)-methylmalonyl-CoA
show the reaction diagram
propionyl-CoA + CO2
(S)-methylmalonyl-CoA
show the reaction diagram
UTP + propanoyl-CoA + HCO3-
UDP + phosphate + (S)-methylmalonyl-CoA
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + propanoyl-CoA + HCO3-
?
show the reaction diagram
-
key enzyme of the 3-hydroxypropanoate cycle
-
-
-
ATP + propanoyl-CoA + HCO3-
ADP + phosphate + (S)-methylmalonyl-CoA
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
10% of the activity with Mg2+
Cs+
-
20 mM, activates, monovalent cation required
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ADP
-
weak inhibition
ATP
Q877I4 and Q877I3 and Q877I5
above 2.0 mM
citrate
DTT
Q877I4 and Q877I3 and Q877I5
5-10 mM, 12% inhibition
K+
Q877I4 and Q877I3 and Q877I5
-
L-alanine
-
-
L-phenylalanine
-
-
L-serine
-
-
L-tryptophan
-
strong inhibitor
L-tyrosine
-
-
L-valine
-
-
malonyl-CoA
methylmalonyl-CoA
Q877I4 and Q877I3 and Q877I5
0.5 mM, 60% inhibition of propionyl-CoA carboxylase
Mg2+
Q877I4 and Q877I3 and Q877I5
above 4.0 mM
Mn2+
Q877I4 and Q877I3 and Q877I5
above 2.0 mM
Na+
Q877I4 and Q877I3 and Q877I5
-
palmitoyl-CoA
-
-
succinyl-CoA
sulfate
Q877I4 and Q877I3 and Q877I5
25 mM, more than 50% inhibition
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
biotin
Q877I4 and Q877I3 and Q877I5
biotin-dependent enzyme
NH4+
-
20 mM, activates, monovalent cation required
palmitoyl-CoA
Q877I4 and Q877I3 and Q877I5
slight stimulative effect on acetyl-CoA carboxylase (116%) and propionyl-CoA carboxylase (135%)
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.05 - 5
acetyl-CoA
0.036 - 0.08
ATP
1.2 - 1.5
Butanoyl-CoA
0.036 - 0.383
Butyryl-CoA
0.3 - 7
HCO3-
0.035 - 2.6
propanoyl-CoA
0.032 - 1.3
propionyl-CoA
1.01
succinyl-CoA
-
pH 7.2, 30C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.66 - 4
acetyl-CoA
2 - 8
propanoyl-CoA
Metallosphaera sedula
-
pH 7.5, 65C
0.47 - 2.86
propionyl-CoA
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.144 - 0.826
acetyl-CoA
0.367 - 26
propionyl-CoA
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.00186
-
cell culture
0.00199
-
cell culture
0.00442
-
cell culture
0.00483
-
cell culture
0.00535
-
cell culture
0.00673
-
cell culture
0.01177
-
cell culture
0.0248
-
cell culture
3.3
-
purified enzyme, pH 7.5, 65C
5.6
-
-
7.54
-
purified mutant enzyme E168K
9.93
-
purified mutant enzyme R165W
9.95
-
purified mutant enzyme R410W
11.9
Q877I4 and Q877I3 and Q877I5
pH 7.5, 70C, propionyl-CoA carboxylase activity
14.13
-
purified enzyme, pH 7.2, 30C
23.35
-
purified wild-type enzyme
27.7
-
-
32.34
-
purified mutant enzyme A497V
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.4 - 6.9
Q877I4 and Q877I3 and Q877I5
at 70C
7.2 - 8.8
-
-
7.5
Q877I4 and Q877I3 and Q877I5
assay at
7.5 - 8.5
-
-
7.5 - 8.3
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.2 - 9.6
-
7.2-8.8: maximal activity, 9.6: about 50% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 40
-
-
65
Q877I4 and Q877I3 and Q877I5
-
70
Q877I4 and Q877I3 and Q877I5
assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50 - 75
Q877I4 and Q877I3 and Q877I5
50C: about 60% of maximal activity, 75C: about 60% of maximal activity
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
; embryo, high level
Manually annotated by BRENDA team
adult, PCC together with methylmalonyl-CoA mutase and in whole rat embryonic central nervous system, both at E15.5 and E18.5; PCCalpha is present in all regions of the central nervous system. PCCalpha is present in the whole embryonic central nervous system, both at E15.5 and E18.5, predominantely in the periventricular zones of telencephalon, midbrain and rhombencephalon
Manually annotated by BRENDA team
adult, highest level, Purkinje and granular layers; pons, medulla and the Purkinje and granular layers
Manually annotated by BRENDA team
; adult and embryo
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
; adult, highest level
Manually annotated by BRENDA team
; adult, highest level
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
adult, highest level, such as the red nucleus and substantia nigra, as well as pons and medulla, and in embryo; red nucleus and substantia nigra
Manually annotated by BRENDA team
; adult, highest level
Manually annotated by BRENDA team
adult, PCC together with methylmalonyl-CoA mutase, basal ganglia; both, methylmalonyl-CoA mutase and PCCalpha enzymes are co-expressed in neurons. PCCalpha is present in neurons of basal ganglia
Manually annotated by BRENDA team
-
developing
Manually annotated by BRENDA team
embryo, in the periventricular zones
Manually annotated by BRENDA team
adult, highest level
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
63400
-
SDS-PAGE
72000
SDS-PAGE, Western blot analysis; Western blot analysis, PCCalpha in the adult brain and liver
450000
-
gel filtration
500000
-
PAGE, gel filtration, sucrose density gradient ultracentrifugation
540000
560000
-
gel filtration
605000 - 615000
-
gel filtration
620000
-
gel filtration
669000
-
alpha4beta4 quaternary structure
690000
-
calculation from sedimentation and diffusion data
730000
-
analytical ultracentrifugation
750000
; gel filtration
800000
additional information
-
contains the tripeptide Pro-Met-Pro, 26 residues towards the amino terminus from the biotin attachment site
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dodecamer
heterododecamer
alpha6beta6-heterododecamer, the alpha-subunit contains the biotin carboxylase and biotin carboxyl carrier protein domains, whereas the beta-subunit supplies the carboxyltransferase activity; the alpha-subunit contains the biotin carboxylase and biotin carboxyl carrier protein domains, whereas the beta-subunit supplies the carboxyltransferase activity
multimer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a PCC chimaera, containing the alpha-subunit of Ruegeria pomeroyi PCC and the beta-subunit of Roseobacter denitrificans PCC is crystallized by the microbatch method under paraffin oil, using 0.1 M HEPES (pH 8.0), 22% (w/v) PEG3350, 0.2 M NaCl and 16% (v/v) glycerol. Crystals of Ruegeria pomeroyi PCC are obtained at 20C by the microbatch method under paraffin oil, using 0.2 M succinic acid (pH 6.5), 22% (w/v) benzamidine and 22% (w/v) PEG3000; microbatch method under oil method
apo and substrate-bound crystal structure of PccB hexamers determined to 2.0-2.8 A. crystallization of PccB in sitting drops at room temperature by vapor diffusion. PccB is the core catalytic beta subunit of the propanoyl-CoA carboxylase multisubunit complex
-
sitting drop vapor diffusion method, mutant enzymes D422V and D422Lwith 0.1 M Tris pH 6.5, 2.0 M (NH4)SO4, mutant enzyme D422N with 0.1 M Bis-Tris pH 6.8, 10% (w/v) MPD, 0.2 M (NH4)OAc, mutant enzyme D422C with 0.1 M Na citrate pH 5.6, 0.2 M (NH4)SO4, and mutant enzyme D422A with 0.1 M Bis-Tris pH 6.2, 20% (w/v) PEG3350, 0.2 M (NH4)SO4
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8.7
-
15 min, stable between 6-8, strong denaturation above pH 8.7, liver enzyme
1878
6.2 - 8.4
-
stable
1868
8 - 9.5
-
maximal stability, mammary gland enzyme
1878
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
-50 - 37
-
stable
0 - 40
-
maximal stability
47
-
30 min, wild-type enzyme is stable, mutant enzyme A497V loses 40% of its activity mutant enzymes R165W, E168K and R410W lose 85% of their activity
50
Q877I4 and Q877I3 and Q877I5
2 h, 40% loss of activity
58
-
the wild-type enzyme undergoes a cooperative two-state transition between the native and denatured states with a Tm of 57.6C
60
Q877I4 and Q877I3 and Q877I5
30 min, 50% loss of activity
70
Q877I4 and Q877I3 and Q877I5
30 min, 90% loss of activity
80
Q877I4 and Q877I3 and Q877I5
30 min, 95% loss of activity
90
Q877I4 and Q877I3 and Q877I5
10 min, complete loss of activity
additional information
-
thermal denaturation is irreversible
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
crude enzyme is relatively unstable
-
limited proteolysis with trypsin results in slow time-dependent deactivation of the enzyme with preferential cleavage of the smaller subunit
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4C, 20 mM phosphate buffer, pH 7.0, 2-4 weeks, no loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Ni-NTA agarose CL-6B resin column chromatography
-
nickel affinity column chromatography
nickel affinity column chromatography and gel filtration; nickel affinity column chromatography and gel filtration
recombinant
recombinant enzymes from Escherichia coli
using Ni-NTA chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
correction of enzyme deficiency in pccA fibroblasts
-
expressed in COS-7 cells at 27C and 37C
-
expressed in Escherichia coli
expressed in Escherichia coli as a His-tagged fusion protein
-
expressed in Escherichia coli as a His-tagged fusion protein. Recombinant PCC, including the His tag are produced and are confirmed to react with clonorchiasis patient sera
-
expressed in Escherichia coli BL21 lambda(DE3) cells
expressed in Escherichia coli; expressed in Escherichia coli
expressed in Saccharomyces cerevisiae
-
expressed using a two hybrid system in COS cells
-
expression in Escherichia coli
-
expression of alpha and beta subunit in Escherichia coli
-
gene encoding the biotin-containing subunit
-
into plasmid pSET152 derivative containing an ermE* promoter, yielding pYJ269, expressed in Streptomyces clavuligerus CKD1119
-
introduced into Streptomyces hygroscopicus UV2-2 strain by conjugation from Escherichia coli ET12567/pUZ8002
-
subunits individually cloned and expressed in Escherichia coli DH5alpha
-
the PccB subunit is expressed in Escherichia coli BL21(DE3) cells
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
in rat embryos (E15.5 and E18.5), methylmalonyl-CoA mutase and PCC show a much higher expression level in the entire central nervous system than in the liver
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A487V
-
no effect on activity
A513_R514insP
D178H
increased alpha/beta subunit ratio, very low activity
DELTA408
catalytically inactive
DELTA499
DELTA514
DELTA531
G246V
-
activity of the mutant enzyme is 12% of the wild-type activity
M442T
catalytically inactive
P228L
increased alpha/beta subunit ratio, very low activity
R165Q
-
beta subunit, no effect on subunit interactions and activity
R44P
catalytically inactive
R67S
-
beta subunit, no effect on subunit interactions only when expressed at low temperature (27C), reduced activity at 37C
W531X
-
activity of the mutant enzyme is less than 1% of the wild-type activity
A431C
-
kcat (propionyl-CoA) decreased compared to wild-type, Km (propionyl-CoA) increased compared to wild-type. kcat (acetyl-CoA) increased compared to wild-type, Km (propionyl-CoA) similar to wild-type
A431D
-
mutant enzyme shows no activity
A431I
-
kcat (propionyl-CoA) decreased compared to wild-type, Km (propionyl-CoA) increased compared to wild-type. kcat (acetyl-CoA) increased compared to wild-type, Km (propionyl-CoA) similar to wild-type
A431L
-
mutant enzyme shows no activity
Y430H/A431I
-
mutant enzyme shows no activity
D440I
the mutation does not change the substrate preference of the enzyme
G668R
the mutation in the biotin carboxyl carrier protein domain abolishes biotinylation
R165Q
the mutation disturbs the recognition of the adenine base of CoA
R165W
the mutation disturbs the recognition of the adenine base of CoA
R399Q
the mutation leads to a large loss in activity
D422A
mutant of the PccB subunit, shows strong preference for butyryl-CoA as substrate
D422C
mutant of the PccB subunit, shows strong preference for butyryl-CoA as substrate
D422I
mutant of the PccB subunit, accepts acetyl-CoA, propionyl-CoA, and butyrl-CoA as substrates, the latter two with lower Vmax/Km values as compared to the wild type enzyme
D422L
mutant of the PccB subunit, the mutants has narrowed down their substrate specificity, accepting only propionyl-CoA as its substrate
D422N
mutant of the PccB subunit, the mutants has narrowed down their substrate specificity, accepting only propionyl-CoA as its substrate
D422V
mutant of the PccB subunit, accepts both propionyl-CoA and butyrl-CoA as substrates but with lower Vmax/Km values as compared to the wild type enzyme
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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