Information on EC 4.1.3.4 - hydroxymethylglutaryl-CoA lyase

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

EC NUMBER
COMMENTARY
4.1.3.4
-
RECOMMENDED NAME
GeneOntology No.
hydroxymethylglutaryl-CoA lyase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
(S)-3-Hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
show the reaction diagram
enzyme is stereospecific and proceeds with inversion of configuration
-
(S)-3-Hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
show the reaction diagram
C237 is crucial for catalysis
-
(S)-3-Hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
show the reaction diagram
identification of reactive cysteines, possibly regulatory mechanism via thiol/disulfide exchange
-
(S)-3-Hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
show the reaction diagram
identification of functionally important S69
-
(S)-3-Hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
show the reaction diagram
identification of reactive cysteines, possibly regulatory mechanism via thiol/disulfide exchange
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
elimination
-
-
of an oxo-acid, C-C bond cleavage
-
enolization
-
-
PATHWAY
KEGG Link
MetaCyc Link
Biosynthesis of secondary metabolites
-
Butanoate metabolism
-
Geraniol degradation
-
ketogenesis
-
leucine degradation I
-
Metabolic pathways
-
mevalonate degradation
-
Synthesis and degradation of ketone bodies
-
Valine, leucine and isoleucine degradation
-
SYSTEMATIC NAME
IUBMB Comments
(S)-3-hydroxy-3-methylglutaryl-CoA acetoacetate-lyase (acetyl-CoA-forming)
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
3-hydroxy-3-methylglutarate-CoA lyase
-
-
-
-
3-hydroxy-3-methylglutarate-CoA lyase
-
-
3-hydroxy-3-methylglutarate-CoA lyase
-
-
3-hydroxy-3-methylglutarate-CoA lyase
P35914
-
3-Hydroxy-3-methylglutaryl CoA cleaving enzyme
-
-
-
-
3-hydroxy-3-methylglutaryl CoA lyase
-
-
3-hydroxy-3-methylglutaryl CoA lyase
-
-
3-hydroxy-3-methylglutaryl CoA lyase
Pseudomonas aeruginosa PAO1SM
-
-
-
3-Hydroxy-3-methylglutaryl coenzyme A lyase
-
-
-
-
3-Hydroxy-3-methylglutaryl-CoA lyase
-
-
-
-
3-Hydroxy-3-methylglutaryl-CoA lyase
-
-
3-Hydroxy-3-methylglutaryl-CoA lyase
P35914
-
3-Hydroxy-3-methylglutaryl-CoA lyase
-
-
3-Hydroxy-3-methylglutaryl-CoA lyase
P97519
-
3-hydroxy-3-methylglutaryl-coenzyme A lyase
-
-
HMG CoA cleavage enzyme
-
-
-
-
HMG CoA lyase
-
-
HMG-CoA lyase
-
-
-
-
HMG-CoA lyase
-
; belongs to the family of DRE-TIM metallolyases
HMG-CoA lyase
P35914
-
HMG-CoA lyase
-
-
HMG-CoA lyase
Pseudomonas aeruginosa PAO1SM
-
-
-
HMGCL
P97519
-
HMGL
P35914
-
Hydroxymethylglutaryl coenzyme A lyase
-
-
-
-
Hydroxymethylglutaryl coenzyme A-cleaving enzyme
-
-
-
-
LiuE protein
-
in addition to show HMG-CoA lyase activity, LiuE also displays 3-hydroxy-3-isohexenylglutaryl-CoA lyase activity
LiuE protein
Pseudomonas aeruginosa PAO1SM
-
in addition to show HMG-CoA lyase activity, LiuE also displays 3-hydroxy-3-isohexenylglutaryl-CoA lyase activity
-
CAS REGISTRY NUMBER
COMMENTARY
9030-83-5
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
duck
-
-
Manually annotated by BRENDA team
bovine
-
-
Manually annotated by BRENDA team
goat
-
-
Manually annotated by BRENDA team
pigeon
-
-
Manually annotated by BRENDA team
E37X is a common HMGCL mutation in Portuguese patients with 3-hydroxy-3-methylglutaric CoA lyase deficiency
-
-
Manually annotated by BRENDA team
human, mitochondrial and peroxisomal enzyme
-
-
Manually annotated by BRENDA team
mitochondrial precursor
UniProt
Manually annotated by BRENDA team
normal and patients with Zellweger syndrome
-
-
Manually annotated by BRENDA team
recombinant enzyme
-
-
Manually annotated by BRENDA team
Spanish patients with the Mediterranean nonsense mutation G109T. The mutation can produce aberrant splicing with three mRNA variants: one of the expected size, the second with deletion of exon 2, and the third with deletion of exons 2 and 3
-
-
Manually annotated by BRENDA team
sheep
-
-
Manually annotated by BRENDA team
strain PAO1SM
-
-
Manually annotated by BRENDA team
Pseudomonas aeruginosa PAO1SM
strain PAO1SM
-
-
Manually annotated by BRENDA team
recombinant enzyme
-
-
Manually annotated by BRENDA team
recombinant wild-type enzyme and C237 mutants
-
-
Manually annotated by BRENDA team
radish
-
-
Manually annotated by BRENDA team
Wistar rat
UniProt
Manually annotated by BRENDA team
pig
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
malfunction
-
3-hydroxy-3-methylglutaryl-coenzyme A lyase deficiency is an inborn error of metabolism characterized by impairment of ketogenesis and leucine catabolism resulting in an organic acidopathy
malfunction
-
3-Hydroxy-3-methylglutaric aciduria is a rare human autosomal recessive disorder caused by deficiency of 3-hydroxy-3-methylglutaryl CoA lyase
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-, O34873
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
P35914
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
ir
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-, Q8YEF2
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
P35914
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
P97519
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
stereochemistry
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
mechanism
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
Pseudomonas aeruginosa PAO1SM
-
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
involved in regulation of isoprenoid pathway
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
involved in ketogenesis, leucine catabolism
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
involved in ketogenesis, leucine catabolism
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
involved in ketogenesis, leucine catabolism
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
leucine catabolism
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
acetoacetate as fuel for extrahepatic tissues, involved in mevalonate synthesis
-
-
-
3-hydroxy-3-methylglutaryl-CoA
acetoacetate + acetyl-CoA
show the reaction diagram
-
-
-
-
-
3-hydroxy-3-methylglutaryl-CoA
acetoacetate + acetyl-CoA
show the reaction diagram
-
-
-
-
?
3-hydroxy-3-methylglutaryl-CoA
acetoacetate + acetyl-CoA
show the reaction diagram
-
-
-
-
-
3-hydroxy-3-methylglutaryl-CoA
acetoacetate + acetyl-CoA
show the reaction diagram
-
-
-
-
-
3-hydroxy-3-methylglutaryl-CoA
acetoacetate + acetyl-CoA
show the reaction diagram
-
-
-
-
-
3-hydroxy-3-methylglutaryl-CoA
acetoacetate + acetyl-CoA
show the reaction diagram
-
-
-
-
?
Acetyl-CoA
?
show the reaction diagram
-
enolization
-
-
-
additional information
?
-
-
last step in ketogenesis
-
?
additional information
?
-
-
last step in ketogenesis
-
?
additional information
?
-
-
last step in ketogenesis
-
?
additional information
?
-
-
last step in ketogenesis
-
?
additional information
?
-
-
last step in ketogenesis
-
?
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)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
-
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
Acetyl-CoA + acetoacetate
show the reaction diagram
P97519
-
-
-
?
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
involved in regulation of isoprenoid pathway
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
involved in ketogenesis, leucine catabolism
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
involved in ketogenesis, leucine catabolism
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
involved in ketogenesis, leucine catabolism
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
leucine catabolism
-
-
-
(S)-3-Hydroxy-3-methylglutaryl-CoA
?
show the reaction diagram
-
acetoacetate as fuel for extrahepatic tissues, involved in mevalonate synthesis
-
-
-
additional information
?
-
-
last step in ketogenesis
-
?
additional information
?
-
-
last step in ketogenesis
-
?
additional information
?
-
-
last step in ketogenesis
-
?
additional information
?
-
-
last step in ketogenesis
-
?
additional information
?
-
-
last step in ketogenesis
-
?
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Bivalent cations
-
-
Bivalent cations
-
required
Bivalent cations
-
stimulate
Ca2+
-
22% activation at 0.1 mM
Cu2+
-
37% activation at 0.1 mM
Cu2+
-
tightly bound, stoichiometry
Cu2+
-
tightly bound to the enzyme
Mg2+
-
possibly involved in coordination of the thioesther carbonyl during catalysis, also stimulates acetyl-CoA enolization
Mg2+
-
330% activation at 0.1 mM
Mg2+
-
required, can be substituted by Mn2+
Mg2+
-
required, Km wild-type enzyme: 0.2mM, Km R41Q mutant: 0.088 mM
Mg2+
-
increases activity at millimolar concentrations
Mg2+
-, O34873
can replace Mn2+ required for activity
Mg2+
-, Q8YEF2
can replace Mn2+ required for activity
Mg2+
-
required for activity
Mn2+
-
290% activation at 0.1 mM
Mn2+
-
required, can be substituted by Mg2+
Mn2+
-
-
Mn2+
-
increases activity at micromolar concentrations
Mn2+
-, O34873
required for activity
Mn2+
-, Q8YEF2
required for activity
Mn2+
-
required for activity
additional information
-
identification of His233, His235, ASp42, and Asn275 as metal-binding ligands
additional information
-, O34873
reaction mechanism involves an invariant Asp-Arg-Glu (DRE)triplet. The Asp ligates the divalent cation, the Arg probably stabilizes charge accumulation in the enolate intermediate, and the Glu maintains the precise structural alignment of the Asp and Arg
additional information
-, Q8YEF2
reaction mechanism involves an invariant Asp-Arg-Glu (DRE)triplet. The Asp ligates the divalent cation, the Arg probably stabilizes charge accumulation in the enolate intermediate, and the Glu maintains the precise structural alignment of the Asp and Arg
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
(R)-3-hydroxy-3-methylglutaryl-CoA
-
-
1,10-phenanthroline
-
43% activity after 4 h at 4 mM
2-Butynoyl-CoA
-
active-site inhibition, only recombinant wild-type, not C237 mutants, indication of active-site directed mutagenesis
2-Butynoyl-CoA
-
sensitivity to inactivation depends on redox state of enzyme, Kinact: 0.22 min-1, reduced, 0.03 min 1, oxidized
3-Hydroxyglutaryl-CoA
-
Ki: 0.05 mM, Ki of acetyl-CoA enolization: 0.095 mM
3-Hydroxyglutaryl-CoA
-
competitive; competitive inhibitor
3-Hydroxyglutaryl-CoA
-
competitive inhibitor
4-Methylnitrobenzene sulfonate
-
sensitivity to inactivation depends on redox state of enzyme, Kinact: 0.178 min-1, reduced, 0.028 min 1, oxidized
acetoacetate
-
-
acetyldithio-CoA
-
-
o-phenanthroline
-
not m-Phenanthroline, probably acts as metal chelator
S-(4-carboxy-3hydroxyisoamyl)-CoA
-
Ki: 0.08 mM
Thiomalic acid
-
-
additional information
-
99% inactivation after air-oxidation, various sulfhydryl-directed agents
-
additional information
-
C323 involved in intersubunit cross-linking upon oxidative inactivation, thiol-disulfide exchange mechanism
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
dithiothreitol
-
8fold stimulation at 5 mM
dithiothreitol
-
activates 2fold at 5 mM
thiols
-
-
thiols
-
required, e.g. cysteine
thiols
-
dithiothreitol or cysteine or mercaptoethanol
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.02
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
pH 8.2, 30C, recombinant enzyme
0.058
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
deletion mutant Mut15, at 37C
0.07
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
wild type enzyme, at 37C
3.1
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
37C, pH 7.5, wild type
6.6
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
37C, pH 7.5, D204N mutant
48
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
wild-type
62
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
R41Q mutant
0.0134
-
3-hydroxy-3-methylglutaryl-CoA
-
K48Q mutant protein, pH not specified in the publication, 30C
0.0209
-
3-hydroxy-3-methylglutaryl-CoA
-
K48N mutant protein, pH not specified in the publication, 30C
0.026
-
3-hydroxy-3-methylglutaryl-CoA
-
pH not specified in the publication, temperature not specified in the publication
0.0265
-
3-hydroxy-3-methylglutaryl-CoA
-
wild type protein, pH not specified in the publication, 30C
0.008
-
hydroxymethylglutaryl-CoA
-
-
0.02
-
hydroxymethylglutaryl-CoA
-
wild-type
0.024
-
hydroxymethylglutaryl-CoA
-
wild-type
0.04
-
hydroxymethylglutaryl-CoA
-
-
0.0448
-
hydroxymethylglutaryl-CoA
-
both isoenzymes
0.045
-
hydroxymethylglutaryl-CoA
-
C323S mutant
0.053
-
hydroxymethylglutaryl-CoA
-
C237A mutant
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0004
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
R41Q mutant
0.105
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
peroxisomal enzyme
0.127
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
mitochondrial enzyme
158
-
(S)-3-hydroxy-3-methylglutaryl-CoA
-
-
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.05
-
3-Hydroxyglutaryl-CoA
-
-
0.021
-
acetoacetate
-
-
0.17
-
acetyldithio-CoA
-
-
0.08
-
S-(4-carboxy-3hydroxyisoamyl)-CoA
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.0018
0.11
-
C237 mutants
0.0098
-
-
-
0.022
-
-
at optimal pH
0.03
-
-
recombinant deletion mutant Mut15, at 37C
0.123
-
-
C170S/C266S mutant protein, pH not specified in the publication, temperature not specified in the publication
0.22
-
-
recombinant deletion mutant Mut12, at 37C
0.224
-
-
C266S mutant protein, pH not specified in the publication, temperature not specified in the publication
1.06
-
-
C170S/C174S mutant protein, pH not specified in the publication, temperature not specified in the publication
1.13
-
-
recombinant deletion mutant Mut3, at 37C
1.2
-
-
recombinant deletion mutant Mut6, at 37C
1.27
-
-
recombinant deletion mutant Mut9, at 37C
1.29
-
-
recombinant wild type enzyme, at 37C
1.3
-
-
-
7
-
-
-
9.5
-
P35914
wild type enzyme, at 37C
18.5
-
-
C170S/C323S mutant protein, pH not specified in the publication, temperature not specified in the publication
21.2
-
-
C197S mutant protein, pH not specified in the publication, temperature not specified in the publication
42
-
-
C141S mutant protein, pH not specified in the publication, temperature not specified in the publication
42.1
-
-
C174S mutant protein, pH not specified in the publication, temperature not specified in the publication
53.1
-
-
C170S mutant protein, pH not specified in the publication, temperature not specified in the publication
80
-
-
wild-type
87.8
-
-
K48N mutant protein, pH not specified in the publication, 30C
100.3
-
-
K48Q mutant protein, pH not specified in the publication, 30C
107
-
-
C323S mutant
114
-
-
wild-type
123
-
-
wild type protein, pH not specified in the publication, temperature not specified in the publication
128
-
-
C234S mutant protein, pH not specified in the publication, temperature not specified in the publication
132
-
-
C307S mutant protein, pH not specified in the publication, temperature not specified in the publication; C323S mutant protein, pH not specified in the publication, temperature not specified in the publication
136
-
-
wild type protein, pH not specified in the publication, 30C
159
-
-
wild-type
220
-
-
peroxisomal enzyme
249
-
-
mitochondrial enzyme
348
-
-
C323S mutant
351
-
-
-
additional information
-
-
activities per g freshweight in mitochondrial and cytosolic fractions
additional information
-
-
organ-specific activities per unit freshweight
additional information
-
-
-
additional information
-
-
tissue distribution of activities
additional information
-
-
enzyme activities from various enzyme deficiency patients and control individuals
additional information
-
-
128.86 nmol/min/g of wet weight liver tissue, 58.49 nmol/min/g of wet weight pancreas tissue, 42.48 nmol/min/g of wet weight kidney tissue, 20.23 nmol/min/g of wet weight testis tissue, 12.6 nmol/min/g of wet weight skeletal muscle, activity not detected in heart and brain
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.4
-
-
enzyme assay at
7.4
-
-
enzyme assay at
8.2
-
-
enzyme assay at
8.2
-
-
enzyme assay at
8.4
-
-
enzyme assay at
8.9
-
-
-
9
9.5
-
both isoenzymes
9.25
-
-
-
10
-
-
-
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.4
10.5
-
-
8
11
-
low activity below pH 8, discussion of kinetic data measured at lower pH
8
9
-
-
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
30
-
-
enzyme assay at
30
-
-
enzyme assay at
30
-
-
-
30
-
-
enzyme assay at
37
-
-
enzyme assay at
pI VALUE
pI VALUE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6.2
-
-
mitochondrial enzyme, isoelectric focusing
7.6
-
-
peroxisomal enzyme, isoelectric focusing
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
13% of activity
Manually annotated by BRENDA team
-
enzyme differs from mitochondrial enzyme according to immunoreactivity and other properties, mitochondrial leader sequence influences quaternary structure
Manually annotated by BRENDA team
-
no activity in lymphoblasts of Zellweger patients
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Bacillus subtilis (strain 168)
Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
31000
-
-
mitochondrial enzyme, SDS-PAGE
31500
-
-
SDS-PAGE, mitochondrial enzyme
31600
-
-
-
32000
-
-
SDS-PAGE
33000
-
-
peroxisomal enzyme, SDS-PAGE
33000
-
-
LiuE His-tagged protein, SDS-PAGE
34100
-
-
peroxisomal enzyme, gel filtration
34100
-
-
SDS-PAGE, peroxisomal enzyme
49000
-
-
gel filtration
64000
-
-
calculated from Stokes' radius
65000
-
-
mitochondrial enzyme, gel filtration
70000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 31600, estimated from nucleotide sequence
?
-
x * 32000, SDS-PAGE
dimer
-
2 * 27000, SDS-PAGE
dimer
-
2 * 32000, mitochondrial enzyme, SDS-PAGE
dimer
-
crosslinking experiments with dibromopopanone
dimer
-, O34873
static light scattering, crystal contains two dimers forming a pseudotetramer per asymmetric unit
dimer
-, Q8YEF2
static light scattering, crystal contains two dimers forming a pseudotetramer per asymmetric unit
hexamer
-
X-ray crystallography, the hexamer consists of three dimers which are supposed to be the physiological enzyme form in solution
homodimer
-
SDS-PAGE (reducing and non-reducing conditions)
tetramer
-
analytical ultracentrifugation, enzyme exists as a mixture of dimers and tetramers
monomer
-
1 * 34500, peroxisomal enzyme, SDS-PAGE
additional information
-
amino acid composition
additional information
-
C323 involved in intersubunit cross-linking upon oxidative inactivation
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
hanging-drop vapour diffusion method; hanging drop vapour diffusion method with 22.5% (w/v) PEG 3350, 210 mM sodium iodide, 5 mM EDTA, 10 mM dithiothreitol
-, O34873
hanging-drop vapour diffusion method; hanging drop vapour diffusion method with 19% (w/v) PEG 3350, 200 mM CaCl2, 10 mM dithiothreitol
-, Q8YEF2
crystal structure at 2.1 A resolution of the recombinant mitochondrial HMG-CoA lyase containing a bound activator cation and 3-hydroxyglutarate. For crystallization experiments, the enzyme is diluted to 5 6 mg/ml. The competitive inhibitor hydroxyglutaryl-CoA is added to the diluted protein at about 1mM concentration. The inhibitor is necessary for generation of uniform diffraction quality crystals. Crystals sufficient for X-ray studies are obtained using an equilibration buffer of 0.1 M Hepes, pH 7.5, 60 mM MgCl2,and 15% polyethylene glycol 8K. The enzyme is mixed 1:1 with the equilibration buffer using sitting drop trays at 19C. Crystals belong to the monoclinic space group C2 with unit cell parameters a = 197.0 A, b = 117.1 A, c = 86.8 A, and beta = 112.5. Six monomers are found in the asymmetric unit; sitting drop vapour diffusion method with 0.1 M HEPES, pH 7.5, 60 mM MgCl2, and 15% polyethylene glycol 8K
-
vapor diffusion method
-
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
30
-
-
rapidly inactivated above
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
extremely unstable, even in presence of glycerol
-
extremely unstable
-
OXIDATION STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
the enzyme is sensitive to oxidation, showing higher activity in reducing conditions
-
681959
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-20C,Tris-HCl buffer, pH 7.1, 30% glycerol, 1 mM dithiothreitol, 6 weeks
-
-80C, potassium phosphate buffer, pH 7.4, at least 6 months
-
-80C, phosphate buffer, pH 7.2, 20% glycerol, several weeks
-
-80C, retains full activity for several months in phosphate buffer containing 20% glycerol at pH 7.2
-
-80C, several weeks
-
-20C, Tris-HCl buffer, pH7.4, 1 mM cysteine, several months
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
partial
-
; nickel-nitrilotriacetic acid column chromatography and Superdex 75 gel filtration
-, O34873
; nickel-nitrilotriacetic acid column chromatography and Superdex 75 gel filtration
-, Q8YEF2
glutathione Sepharose column chromatography
-
immobilized metal ion affinity chromatography (Ni2+)
-
mitochondrial and peroxisomal enzyme
-
Q-Sepharose column chromatography, phenyl-agarose column chromatography, and Superose 12 column chromatography
-
recombinant wild-type enzyme and C323S mutant
-
overexpressed in Escherichia coli, immunoreaction with avian liver enzyme antibodies
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression in Escherichia coli
-, O34873
expression in Escherichia coli
-, Q8YEF2
nucleotide sequence
-
expressed in Escherichia coli
-
expressed in Escherichia coli BL21 cells
-
expressed in Escherichia coli JM105 cells
P35914
expressed in Escherichia coli; mitochondrial and peroxisomal enzyme
-
expressed in Escherichia coli; overexpression of wild-type enzyme and synthetic C323 mutant
-
His-tagged version
-
His-tagged version expressed in Escherichia coli BL21(DE3)
-
nucleotide sequence, identification of a 2-base pair deletion in S69 codon of enzyme-deficient patients
-
expressed as His-tagged recombinant protein in Escherichia coli pTrcAtuE cells
-
expressed in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
C240A
-, O34873
increased Km relative to the wild type enzyme
C240S
-, O34873
decreased Km relative to the wild type enzyme
D16E
-, O34873
decreased Km relative to the wild type enzyme
D16N
-, O34873
decreased Km relative to the wild type enzyme
D178A
-, O34873
increased Km relative to the wild type enzyme
D254A
-, O34873
decreased Km relative to the wild type enzyme
E11D
-, O34873
decreased Km relative to the wild type enzyme
E253A
-, O34873
decreased Km relative to the wild type enzyme
E46A
-, O34873
increased Km relative to the wild type enzyme
H207A
-, O34873
increased Km relative to the wild type enzyme
H207D
-, O34873
increased Km relative to the wild type enzyme
H207R
-, O34873
decreased Km relative to the wild type enzyme
K297S
-, O34873
increased Km relative to the wild type enzyme
R15Q
-, O34873
increased Km relative to the wild type enzyme
A252A
-, Q8YEF2
decreased Km relative to the wild type enzyme
C238A
-, Q8YEF2
increased Km relative to the wild type enzyme
C238S
-, Q8YEF2
decreased Km relative to the wild type enzyme
D14E
-, Q8YEF2
decreased Km relative to the wild type enzyme
D176A
-, Q8YEF2
increased Km relative to the wild type enzyme
E44A
-, Q8YEF2
increased Km relative to the wild type enzyme
E9D
-, Q8YEF2
decreased Km relative to the wild type enzyme
H205A
-, Q8YEF2
increased Km relative to the wild type enzyme
H205D
-, Q8YEF2
increased Km relative to the wild type enzyme
H205R
-, Q8YEF2
decreased Km relative to the wild type enzyme
R13Q
-, Q8YEF2
increased Km relative to the wild type enzyme
V251A
-, Q8YEF2
decreased Km relative to the wild type enzyme
C141S
-
strong inter-subunit dimer formation (SDS-PAGE, non-reducing conditions)
C170S
-
inter-subunit dimer formation not observed (SDS-PAGE, non-reducing conditions)
C170S/C174S
-
moderate inter-subunit dimer formation (SDS-PAGE, non-reducing conditions)
C170S/C266S
-
inter-subunit dimer formation not observed (SDS-PAGE, non-reducing conditions)
C170S/C323S
-
inter-subunit dimer formation not observed (SDS-PAGE, non-reducing conditions)
C174S
-
moderate inter-subunit dimer formation (SDS-PAGE, non-reducing conditions)
C197S
-
weak inter-subunit dimer formation (SDS-PAGE, non-reducing conditions)
C234S
-
weak inter-subunit dimer formation (SDS-PAGE, non-reducing conditions)
C266S
-
inter-subunit dimer formation not observed (SDS-PAGE, non-reducing conditions)
C307S
-
moderate inter-subunit dimer formation (SDS-PAGE, non-reducing conditions)
C323S
-
shows less dithiothreitol activation than wild-type enzyme
C323S
-
inter-subunit dimer formation not observed (SDS-PAGE, non-reducing conditions)
D204N
-
reduced catalytic efficiency, mutation causes 3-hydroxy-3-methylgluratic aciduria in vivo
D204N
-
decreased activity
D204N
-
lack of enzymatic activity
D42A
-
4fold decrease in proton exchange
D42A
-
exhibits catalytic rates diminished by 130000fold
D42H
-
decreased activity
D42H
-
lack of enzymatic activity
E279K
-
unstable recombinant protein
E279K
-
lack of enzymatic activity
E37X
-
E37X is a common HMGCL mutation in Portuguese patients with 3-hydroxy-3-methylglutaric CoA lyase deficiency
G109T
-
Spanish patients with the Mediterranean nonsense mutation G109T. The mutation can produce aberrant splicing with three mRNA variants: one of the expected size, the second with deletion of exon 2, and the third with deletion of exons 2 and 3
G203E
P35914
the mutation causes 3-hydroxy-3-methylglutaric aciduria, it has less than 0.02% of the wild type enzyme activity
G203E
-
lack of enzymatic activity
H233A
-
10fold decrease in proton exchange
H233A
-
exhibits catalytic rates diminished by 6400fold
H233R
-
decreased activity
H233R
-
lack of enzymatic activity
K48N
-
the mutation causes 3-hydroxy-3-methylglutaric aciduria, shows less than 2% of wild type HMG-CoA lyase activity
K48N
-
lack of enzymatic activity
K48N
-
inherited mutation
K48Q
-
mimics Lys acetylation
R41M
-
lower activity than R41Q mutant
R41M
-
catalytically deficient
R41Q
-
mutation leads to human HMG-CoA lyase deficiency
R41Q
-
decreased activity
R41Q
-
missense mutation causing 3-hydroxy-3-methylglutaric aciduria
R41Q
-
lack of enzymatic activity
S201Y
-
no catalytic efficiency, mutation causes 3-hydroxy-3-methylgluratic aciduria in vivo
S201Y
-
no activity
S201Y
-
lack of enzymatic activity
S75R
-
no catalytic efficiency, mutation causes 3-hydroxy-3-methylgluratic aciduria in vivo
S75R
-
no activity
S75R
-
lack of enzymatic activity
V70L
-
lack of enzymatic activity
L263P
-
lack of enzymatic activity
additional information
-
the deletion mutant Mut15 (last 15 C-terminal residues deleted) shows less than 2% specific activity, the deletion mutant Mut12 (last 12 C-terminal residues deleted) shows 17% specific activity, the deletion mutant Mut9 (last 9 C-terminal residues deleted) shows 99% specific activity, the deletion mutant Mut6 (last 6 C-terminal residues deleted) shows 93% specific activity, the deletion mutant Mut3 (last 3 C-terminal residues deleted) shows 88% specific activity, compared to the wild type enzyme, respectively
additional information
-
c.494G to T, p.Arg165Gln, missense mutation in the 3-hydroxy-3-methylglutaryl CoA lyase gene; IVS3+1G to A, slice site mutation; IVS6-1G to A slice site mutation
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
medicine
-, O34873
mutations in this enzyme cause a human autosomal recessive disorder called primary metabolic aciduria
medicine
-, Q8YEF2
mutations in this enzyme cause a human autosomal recessive disorder called primary metabolic aciduria
medicine
-
3-hydroxy-3-methylglutaryl-coenzyme A lyase deficiency may cause hypoglycaemia which can lead to death
medicine
-
genetically heterogeneous deficiency, participation of S69 codon 2-base pair deletion in some cases
medicine
-
3-hydroxy-3-methylglutaryl CoA lyase deficiency is a rare autosomal recessive mitochondrial disease characterized by a deficiency in the enzyme 3-hydroxy-3-methylglutaryl CoA lyase
medicine
-
dilated cardiomyopathy is associated with HMG CoA lyase deficiency
medicine
-
3-hydroxy-3-methylglutaryl-coenzyme A lyase deficiency is a rare inborn error affecting leucine catabolism and ketogenesis, usually presenting in the neonatal period
medicine
P97519
3-hydroxy-3-methylglutaryl CoA lyase deficiency is a rare autosomal recessive mitochondrial disease characterized by a deficiency in the enzyme 3-hydroxy-3-methylglutaryl CoA lyase
medicine
-
3-hydroxy-3-methylglutaric aciduria is an autosomal recessive branched chain organic aciduria caused by the deficiency of the enzyme 3-hydroxy-3-methylglutaryl-CoA lyase