Information on EC 4.2.2.10 - pectin lyase

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

EC NUMBER
COMMENTARY hide
4.2.2.10
-
RECOMMENDED NAME
GeneOntology No.
pectin lyase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Eliminative cleavage of (1->4)-alpha-D-galacturonan methyl ester to give oligosaccharides with 4-deoxy-6-O-methyl-alpha-D-galact-4-enuronosyl groups at their non-reducing ends
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
beta-elimination
elimination
ester hydrolysis
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
pectin degradation I
-
-
SYSTEMATIC NAME
IUBMB Comments
(1->4)-6-O-methyl-alpha-D-galacturonan lyase
Favours pectin, the methyl ester, over pectate, the anion (which is the preferred substrate of EC 4.2.2.2, pectate lyase). Demethylation progressively slows its action; it can nevertheless cleave on either side of a demethylated residue if the residue at the other end of the scissile bond is methylated.
CAS REGISTRY NUMBER
COMMENTARY hide
9033-35-6
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain MTCC 7589
-
-
Manually annotated by BRENDA team
strain CCT 3232
-
-
Manually annotated by BRENDA team
mutant strain
-
-
Manually annotated by BRENDA team
strain 148
-
-
Manually annotated by BRENDA team
strain 4M-147
-
-
Manually annotated by BRENDA team
strain NCIM 548
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain MTCC 7588
-
-
Manually annotated by BRENDA team
strain MTCC 7588
-
-
Manually annotated by BRENDA team
-
AY825251
GenBank
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain BP-7
-
-
Manually annotated by BRENDA team
strain DT7
-
-
Manually annotated by BRENDA team
strain PN 33
-
-
Manually annotated by BRENDA team
PN33
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain NRRL 13884, inducible enzyme
-
-
Manually annotated by BRENDA team
strain NRRL 13884, inducible enzyme
-
-
Manually annotated by BRENDA team
strain PPY-1
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Erwinia aroidea
AMS 6082
-
-
Manually annotated by BRENDA team
Erwinia aroidea AMS 6082
AMS 6082
-
-
Manually annotated by BRENDA team
strain 185
-
-
Manually annotated by BRENDA team
strain 185
-
-
Manually annotated by BRENDA team
2389
-
-
Manually annotated by BRENDA team
strain PPY-5 and PPY6
-
-
Manually annotated by BRENDA team
strain PPY-5 and PPY6
-
-
Manually annotated by BRENDA team
no activity in Aspergillus japonicus
-
-
-
Manually annotated by BRENDA team
strain BP-23
-
-
Manually annotated by BRENDA team
strain BP-23
-
-
Manually annotated by BRENDA team
strain Res 23-10
-
-
Manually annotated by BRENDA team
strain MTCC 8897
-
-
Manually annotated by BRENDA team
strain MTCC 8897
-
-
Manually annotated by BRENDA team
strain F16
-
-
Manually annotated by BRENDA team
strain CCT6421
-
-
Manually annotated by BRENDA team
CECT 2294
-
-
Manually annotated by BRENDA team
strain CF2
-
-
Manually annotated by BRENDA team
strain RFC3
-
-
Manually annotated by BRENDA team
strain FT-28
-
-
Manually annotated by BRENDA team
strain FT-28
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain RA-17
-
-
Manually annotated by BRENDA team
strain RA-17
-
-
Manually annotated by BRENDA team
strain 168, strain 147, strain FT-01 and strain 36
-
-
Manually annotated by BRENDA team
lemon isolate, orange isolate, mosambi isolate
-
-
Manually annotated by BRENDA team
Hevea brasiliensis trees infected with
-
-
Manually annotated by BRENDA team
strain SL-125
-
-
Manually annotated by BRENDA team
strain SL-125
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
(6-O-CH3-GalpA)4
?
show the reaction diagram
(6-O-CH3-GalpA)5
?
show the reaction diagram
(6-O-CH3-GalpA)6
?
show the reaction diagram
(6-O-CH3-GalpA)7
?
show the reaction diagram
(6-O-CH3-GalpA)8
?
show the reaction diagram
-
-
-
-
?
(6-O-CH3-GalpA)9
?
show the reaction diagram
-
best substrate
-
-
?
4-nitrophenyl alpha-D-glucopyranoside
?
show the reaction diagram
-
-
-
-
?
apple pectin
?
show the reaction diagram
arabinan
?
show the reaction diagram
-
-
-
-
?
citrus pectin
?
show the reaction diagram
DELTA4,5-(6-O-CH3-GalpA)4
?
show the reaction diagram
-
-
-
-
?
DELTA4,5-(6-O-CH3-GalpA)5
?
show the reaction diagram
-
-
-
-
?
DELTA4,5-(6-O-CH3-GalpA)6
?
show the reaction diagram
-
-
-
-
?
galacturonic acid
?
show the reaction diagram
methoxylated pectic acid
?
show the reaction diagram
oat spelt xylan
?
show the reaction diagram
-
-
-
-
?
orange waste
?
show the reaction diagram
partially methyl-esterified pectin
?
show the reaction diagram
prepared from citrus and Aspergillus sp.
-
-
?
pectin
4,5-unsaturated oligogalacturonates
show the reaction diagram
pectin
?
show the reaction diagram
pectin
DELTA4,5-unsaturated oligosaccharides
show the reaction diagram
pectin
unsaturated methyloligogalacturonates
show the reaction diagram
pectin
unsaturated uronide + H2O
show the reaction diagram
-
-
-
-
?
polygalacturonic acid
?
show the reaction diagram
polygalacturonic acid + H2O
?
show the reaction diagram
-
low activity
-
-
?
polymethyl polygalacturonate methyl glycoside
?
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
pectin
?
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2-mercaptoethanol
-
activates 1.5fold at 100 mM
Ba2+
Erwinia aroidea
-
0.45 mM, slight stimulation
CaCl2
-
activates the purified enzyme by 50% at 1-100 mM, activates at 0.005% in the culture medium, activation is lowered in presence of MgSO4
Hg2+
-
stimulates
MgSO4
-
no effect on purified enzyme, activates at 0.005% in the culture medium, activation is lowered in presence of CaCl2
Sodium arsenate
-
slightly promotes the activity of PNL (110% relative activity at 1 mM)
Sr2+
Erwinia aroidea
-
0.45 mM, slight stimulation
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
acetate
-
-
Ag2+
-
complete inhibition
Al3+
-
10 mM, 5% residual activity
CaCl2
-
slight inhibition at 100 mM
Cinnamic acid
-
enzyme activitiy of pectin lyase decreases significantly when 0.1 mg/l of cinnamlic acid is added
coumaric acid
-
enzyme activitiy of pectin lyase decreases significantly when 0.1 mg/l of coumaric acid is added
diethyldicarbonate
-
1 mM, complete inactivation
dithiothreitol
-
-
endogenous enzyme inhibitor protein
-
MW of 25 kDa, loss of 70% activity after treatment with trypsin, unaffected by DNase I and RNase A, loss of 65% activity after heating to 95°C for 5 min
-
ferulic acid
-
enzyme activitiy of pectin lyase decreases significantly when 0.1 mg/l of ferulic acid is added
formate
-
-
gallic acid
-
enzyme activitiy of pectin lyase decreases significantly when 0.1 mg/l of gallic acid is added
H2O2
-
5 mM, 29% inhibition
Iodine
iodoacetate
-
-
iso-butyrate
-
-
K4[Fe(CN)6]
KMnO4
malic anhydride
-
2 mM, complete inhibition
N-bromosuccinimide
n-Butyrate
-
-
N-Chlorosuccinimide
-
2 mM, 21% inhibition
NAD+
-
above 0.25 mM
NEM
-
2 mM, 96% inhibition
Ni2+
-
10 mM, 24% residual activity
p-Chloromercuriphenylsulfonic acid
-
2 mM, complete inhibition
Pectin
-
substrate inhibition
Phenylmethylsulfonylfluoride
potassium ferrocyanide
potassium permanganate
propionate
-
-
Sodium arsenate
Sodium azide
Tannic acid
-
-
trans-caffeate
-
enzyme activitiy of pectin lyase decreases significantly when 0.1 mg/l of caffic acid is added
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanol
-
10 mM, 124% of initial activity
alpha-expansin
-
alpha-expansin synergistically enhances the degradation activity of recombinant pectinase Pel1
-
cAMP
-
enzyme induction at 5-10 mM
Co2+
-
25% increase of activity at 1 mM
EDTA
-
1 mM, 123% of initial activity
iodoacetate
-
10 mM, stimulates
L-cystine
-
5 mM, 142% of initial activity
mitomycin C
-
temperature-dependent induction of enzyme production, optimal at 30°C
Sodium arsenate
yeast extract components
-
induction of enzyme production by at least one organic component of yeast extract from sucrose containing culture medium, component is soluble in the nucleotide fraction, compound is thermostable, polar, dialyzable at 2000 Da, hydrolyzable by HCl, activated by boiling for up to 60 min
-
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.35
Pectin
-
pH 5.0, 45°C
additional information
apple pectin
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
66 - 110
citrus pectin
-
0.83 - 110
Pectin
20
pectin 26% methylated
Aspergillus japonicus
-
pH 5.0, 40°C
-
77
pectin 65% methylated
Aspergillus japonicus
-
pH 5.0, 40°C
-
86
pectin 89% methylated
Aspergillus japonicus
-
pH 5.0, 40°C
-
additional information
additional information
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.316
-
crude enzyme, in 100 mM sodium phosphate buffer (pH 8.0), at 37°C
1.5
-
crude extract
4.5
-
pH 7.0, 37°C
8.9
-
purified enzyme, acetate buffer 50 mM
12.9
-
after 8.6fold purification
18.33
-
after 58.01fold purification, in 100 mM sodium phosphate buffer (pH 8.0), at 37°C
32
-
purified enzyme, McIlvaine buffer with 0.1 M citrate and 0.2 M phosphate
148
-
recombinant enzyme in Escherichia coli cell supernatant
175
-
pH 8.0,temperature not specified in the publication
297
AY825251
pH 10, 60°C
1433
-
purified enzyme
1502
-
purified recombinant enzyme
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.6
-
assay at
5.2
-
soluble enzyme
5.5 - 6.5
-
-
5.6
-
soluble enzyme form
6.2
-
and a second optimum at pH 6.9, immobilized enzyme
6.9
-
and a second optimum at pH 6.2, immobilized enzyme
8 - 8.2
Erwinia aroidea
-
-
8.8
-
enzyme form PL I, sodium polypectate medium
9.3
-
enzyme form PL I, cell wall medium
9.8
-
enzyme form PL II, sodium polypectate medium or cell wall medium
10
AY825251
-
additional information
-
a bell shaped pH profile at low substrate concentrations, shifts of the pH optimum to more basic values upon increasing substrate concentrations accompanied by deviation of the profile from a bell shaped curve
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3 - 11
-
more than 90% of maximum activity within
4 - 6.5
-
50% of maximal activity at pH 4.0 and pH 6.5
4 - 9
-
; the enzyme retains approximately 100% of its maximum activity for 24 h in a buffer of pH range 4.0-9.0
4.3 - 6.3
-
pH 4.3: about 50% of maximal activity, pH 6.3: about 50% of maximal activity
4.8 - 8.3
-
pH 4.8: about 35% of maximal activity, pH 8.3: about 55% of maximal activity
5 - 7.5
-
pH 5: 55% of maximal activity, pH 7.5: 35% of maximal activity
8 - 8.5
-
citrus pectin, Tris-HCl buffer
8.5 - 10
-
pH 8.5: about 30% of maximal activity, pH 10: about 60% of maximal activity, enzyme form PL I, polypectate culture filtrate
8.5 - 10.5
-
pH 8.5: about 50% of maximal activity, pH 10.5: about 40% of maximal activity, enzyme form PL II, polypectate culture filtrate
9 - 10.5
AY825251
more than 50% of maximum activity within
9 - 12
-
the enzyme retains activity in the pH 9.0-12.0 range when exposed for 24 h
additional information
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35 - 40
37
-
recombinant His-tagged enzyme
38
-
assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10 - 40
-
10°C: high activity, 40°C: optimum
20 - 55
-
20°C: about 40% of maximal activity, 55°C: about 70% of maximal activity
20 - 50
-
20°C: about 50% of maximal activity, 45°C: about 65% of maximal activity, 50°C: about 35% of maximal activity
30 - 65
-
30°C: about 45% of maximal activity, 65°C: about 35% of maximal activity
30 - 50
40 - 60
-
-
40 - 65
-
40°C: about 50% of maximal activity, 65°C: about 70% of maximal activity
55 - 65
AY825251
more than 60% of maximum activity within
additional information
-
-
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
-
calculated from sequence
7.7
-
isoelectric focusing
8
-
isoelectric focusing
8.6
-
isoelectric focusing
9.4
-
isoelectric focusing
additional information
-
pI of the proteins contained in the partially purified enzyme preparation, isoelectric focusing
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
in medium containing sodium polypectate or cell walls from Phaseolus vulgaris
Manually annotated by BRENDA team
-
infected of Hevea brasiliensis trees infected with Thanatephorus cucumis
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
PnlH, is exported by the Tat system and targeted to the outer membrane by its uncleaved N-terminal Tat signal anchor
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22000
-
gel filtration
23000 - 23500
-
enzyme form PL I, gel filtration
23000
-
SDS-PAGE
23500 - 28500
-
SDS-PAGE
25000
-
gel filtration
27000 - 28500
-
enzyme form PL II, gel filtration
28000 - 32000
Erwinia aroidea
-
gel filtration
31600
-
SDS-PAGE
34200
-
1 * 34200, SDS-PAGE
35400 - 36800
-
type II enzyme, gel filtration
35500 - 37950
-
type I enzyme, gel filtration
35880
AY825251
MALDI-TOF/TOF
37400
x * 37400, calculated
37546
-
x * 37546, calculated from sequence
39000
-
gel filtration
40000
-
x * 40000, SDS-PAGE
44000
-
x * 44000, nonglycosylated recombinant enzyme, x * 48000, glycosylated recombinant enzyme
48000
-
x * 44000, nonglycosylated recombinant enzyme, x * 48000, glycosylated recombinant enzyme
105000
-
x * 105000, SDS-PAGE
106000
-
x * 106000, SDS-PAGE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glycoprotein
side-chain modification
-
2.5% sugar content, based on weight. Type I enzyme contains only mannose residues, 4 mol/mol. Type II enzyme can be separated into two species which are different in their ratio of mannose to glucose residues
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1.5
-
30°C, 24 h, 46% loss of activity
34013
3 - 11
-
-
729668
3.9
-
minimum deactivation rate constant at pH 3.9 and 29°C, deactivation process is modelled as first-order kinetics
654468
4 - 10
-
the enzyme is stable for 24 h in the pH range 4.0-10.0
701027
4 - 5
-
30°C, stable
34011
4 - 8.5
-
30 min, 40°C, stable
114105
4 - 7
-
4°C or 30°C, stable
34013
5
-
4°C, 24 h, stable
34020
5 - 8.8
-
2 h, stable
34004
5 - 6
-
highest stability, 20% loss of activity after 3 h at 40°C. 40% loss of activity after 3 h at 50°C
678507
5.2 - 8.1
-
stable
34017
5.5 - 6
-
good stability at pH 5.5-6.0
701703
6 - 10
6 - 9
-
enzyme is optimally stable at pH 7.5-8.5, 50% activity at neutral pH, complete loss of activity occurs below pH 6.0 and above pH 9.0
657403
7
-
4°C, 24 h, about 30% loss of activity
34020
7 - 8.5
Erwinia aroidea
-
30°C, 36 h, no appreciable loss of activity
34012
7
-
4°C, 24 h, about 35% loss of activity
34008
7.5 - 9.5
-
good stability
680118
8 - 11
AY825251
-
728987
9
-
4°C, 24 h, complete loss of activity
34008
10.5
-
4°C, 313 h, 7% loss of activity
34019
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
-
stable for 1 h
20
-
room temperature, 5 min, 30% loss of activity
22
-
pH-range 6.0-10, 24 h, more than 85% of initial activity
25
-
t1/2 for soluble enzyme: 6 h, t1/2 for the immobilized enzyme: more than 30 days
29
-
minimum deactivation rate constant at pH 3.9 and 29°C, deactivation process is modelled as first-order kinetics
35
-
t1/2 for soluble enzyme: 1 h, t1/2 for the immobilized enzyme: more than 22 days
36
-
10 min, 30% loss of activity
42
-
5 min, 30% loss of activity
45 - 50
-
the pectin lyase activity shows thermal stability, with half-lives of 30 and 27 min when incubated at 45 and 50°C, respectively
50 - 70
-
the enzyme does not loose activity up to 50°C if exposed for 1 h, addition of ammonium sulfate in the range of 0.1-2.0 M increases the thermostability of the enzyme with 0.6 and 1.8 M of ammonium sulfate providing complete stability at 60 and 70°C. respectively, 40% of activity is recovered after incubating the purified enzyme at 60°C for 1 h, while there is 12% of activity recovered after incubation at 70°C for 1 h
50 - 60
-
the enzyme retains its full activity up to 50°C, and thereafter, activity decreased with increase in temperature, however 75% of the activity is lost after incubating the purified PNL at 60°C for 1 h; the enzyme retains its full activity up to 50°C, and thereafter, activity decreases with increase in temperature, 75% of the activity is lost after incubating the purified PNL at 60°C for 1 h, the half-lives at 60, 70, 80, and 85°C are 7.03, 3.9, 1.8, and 0.89 min, respectively
68
-
pH 7.8, 5 min, 97% loss of activity
additional information