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Enzyme Nomenclature
Information on EC 4.2.2.2 - pectate lyase
for references in articles please use BRENDA:EC4.2.2.2
Word Map on EC 4.2.2.2
- 4.2.2.2
- erwinia
- chrysanthemi
-
lyases
- polygalacturonase
- carotovora
- cellulase
-
macer
-
phytopathogenic
- pectinase
-
pectinolytic
-
soft-rotting
- atroseptica
-
methylesterase
- xylanase
- polypectate
-
beta-helix
- dadantii
- dickeya
-
4,5-unsaturated
-
pathovars
-
wall-degrading
-
harpins
- pectobacterium
-
trigalacturonic
- digalacturonate
-
plant-parasitic
- gloeosporioides
- oligogalacturonates
-
pectin-degrading
-
enterobacterium
-
degumming
- ramie
- pectinesterase
-
homogalacturonan
-
alkaliphilic
- degradation
- agriculture
- food industry
- environmental protection
-
expansins
- biotechnology
- molecular biology
- industry
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
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EC NUMBER 
COMMENTARY 
4.2.2.2
-
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RECOMMENDED NAME
GeneOntology No.
pectate lyase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
elimination
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
(1->4)-alpha-D-galacturonan lyase
Favours pectate, the anion, over pectin, the methyl ester (which is the preferred substrate of EC 4.2.2.10, pectin lyase).
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CAS REGISTRY NUMBER
COMMENTARY
9015-75-2
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Bacillus sp. (in: Bacteria) KSM-P15
isolated from soil of a saline-alkaline field in Tianjin, China, gene Bsu11286Pel
-
-
isolated from soil of Flaming Mountain in the Turpan Basin of Xinjiang, China, gene pl-str
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gene pelB cloned from the metagenomic DNA of alkaline environment soils
UniProt
an endo-pectate lyase produced by a genetically modified Bacillus sp. is used
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isolated from soil of a saline-alkaline field in Tianjin, China, gene Bsu11286Pel
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3937; at least 7 isoenzymes, 5 major isoenzymes, PelA, PelB, PelC, PelD, Pel E and two minor isoenzyme PelL and PelZ
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Lysinibacillus fusiformis, isolated from fermenting cocoa beans
UniProt
3 isoenzymes; subsp. atroseptica, 3 isoenzymes; subsp. carotovora
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formerly Erwinia aroideae; pectate lyase I and pectate lyase II
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-
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
physiological function
additional information
evolution
-
pectate lyase 2 sequence analysis and evolutionary analysis, overview
evolution
pectate lyase 2 sequence analysis and evolutionary analysis, overview
evolution
pectate lyase 2 sequence analysis and evolutionary analysis, overview
evolution
pectate lyase 2 sequence analysis and evolutionary analysis, overview
evolution
-
parallel beta-helix, active site residues, and substrate binding cleft are similar to those in the other pectate lyases from polysaccharide lyase family 1, PL1
evolution
-
the mature Apel is structurally related to the enzymes in the polysaccharide lyase family 1
evolution
-
Dickeya dadantii pectate lyases belong to different families, namely, PL1, PL2, PL3, and PL9, PelN belongs to the PL9 family. The PelN orthologue is encoded by all of the sequenced genomes of the Dickeya and Pectobacterium species. The PelN structural model, constructed on the basis of the PelL structure, suggests that the PelL global topology and its catalytic amino acids are conserved in PelN. Notable differences concern the presence of additional loops at the PelN surface, and the replacement of PelL charged residues, involved in substrate binding, by aromatic residues in PelN
evolution
-
parallel beta-helix, active site residues, and substrate binding cleft are similar to those in the other pectate lyases from polysaccharide lyase family 1, PL1
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evolution
-
the mature Apel is structurally related to the enzymes in the polysaccharide lyase family 1
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malfunction
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type II secretion system-deficient mutant of Dickeya dadantii 3937, A1919, DELTA ouC, loses the capability to promote the multiplication of EDL933, whereas Ech159, DELTApoS, a stress-responsive sigma-factor RpoS-deficient mutant, increases EDL933 proliferation on lettuce leaves 2fold mor than the wild-type strain. Mutant A1919 is completely deficient in the secretion of pectate lyases, which play a major role in plant tissue maceration
malfunction
-
construction of CcpelA gene-disrupted mutants, the mutants show reduced aggressiveness towards tomato fruits and impaired pectate lyase secretion and extracellular activity, while overexpression of CcpelA in the Si-60 isolate increases its aggressiveness and PL secretion, overview
malfunction
-
no significant difference is detected after infection of potato tubers, but a weak decrease in the degree of maceration of chicory leaves is caused by the pelN mutant compared to the wild-type strain
malfunction
gene inactivation does not result in complete loss of pectate lyase activity, but the symptoms of anthracnose in the infected host plants are reduced
malfunction
-
type II secretion system-deficient mutant of Dickeya dadantii 3937, A1919, DELTA ouC, loses the capability to promote the multiplication of EDL933, whereas Ech159, DELTApoS, a stress-responsive sigma-factor RpoS-deficient mutant, increases EDL933 proliferation on lettuce leaves 2fold mor than the wild-type strain. Mutant A1919 is completely deficient in the secretion of pectate lyases, which play a major role in plant tissue maceration
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physiological function
PEL may play an important role in the process of normal fiber elongation in cotton
physiological function
-
pectate lyase is involved in cell wall hydrolysis and pulp softening during ripening fruits
physiological function
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the influence of the virulence mechanisms of Dickeya dadantii strain 3937, a broad-host-range phytopathogen, on the proliferation of the human pathogen Escherichia coli O157:H7 EDL933 on postharvest lettuce, strain 3937 promotes the multiplication of EDL933, overview
physiological function
-
pectate lyase 2 degrades the unesterified polygalacturonate pectate of the host cell wall
physiological function
pectate lyase 2 degrades the unesterified polygalacturonate pectate of the host cell wall
physiological function
pectate lyase 2 degrades the unesterified polygalacturonate pectate of the host cell wall
physiological function
pectate lyase 2 degrades the unesterified polygalacturonate pectate of the host cell wall
physiological function
-
role of secreted pectate lyase, a cell wall-degrading enzyme, in the aggressiveness of Colletotrichum coccodes, overview
physiological function
the organism causes anthracnose in infected bean plants, pectate lyase encoded by the pecCl1 gene is an important determinant for the aggressiveness of Colletotrichum lindemuthianum
physiological function
-
the influence of the virulence mechanisms of Dickeya dadantii strain 3937, a broad-host-range phytopathogen, on the proliferation of the human pathogen Escherichia coli O157:H7 EDL933 on postharvest lettuce, strain 3937 promotes the multiplication of EDL933, overview
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physiological function
-
pectate lyase is involved in cell wall hydrolysis and pulp softening during ripening fruits
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additional information
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RpoS, the general stress response sigma-factor involved in cell survival in suboptimal conditions, plays a role in EDL933 proliferation by controlling the production of pectate lyases in Dickeya dadantii 3937, e.g. via negative regulation of pelD promoter activity
additional information
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implication of Bacillus sp. in the production of pectinolytic enzymes during cocoa fermentation
additional information
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implication of Bacillus sp. in the production of pectinolytic enzymes during cocoa fermentation
additional information
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implication of Bacillus sp. in the production of pectinolytic enzymes during cocoa fermentation
additional information
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implication of Bacillus sp. in the production of pectinolytic enzymes during cocoa fermentation
additional information
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implication of Bacillus sp. in the production of pectinolytic enzymes during cocoa fermentation
additional information
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implication of Bacillus sp. in the production of pectinolytic enzymes during cocoa fermentation
additional information
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the organism is the soft rot pathogen of calla lily growing around Kunming, soft rot is a major disease of calla lily, Zantedeschia spp., and other important crops worldwide. The pectate lyase contributes to the disease by tuber maceration cleaving structural pectic polymers, overview
additional information
-
the enzyme from Xanthomonas campestris ACCC 10048 is a low-temperature-active alkaline pectate lyase
additional information
invariant amino acids involved in catalytic function mainly comprised the catalytic residues R275, K244, and R280, and the Ca2+-binding residues D151, D173, and D177 in PelN
additional information
-
the PelN structural model, constructed on the basis of the PelL structure, suggests that the PelL global topology and its catalytic amino acids are conserved in PelN. Notable differences concern the presence of additional loops at the PelN surface, and the replacement of PelL charged residues, involved in substrate binding, by aromatic residues in PelN
additional information
-
RpoS, the general stress response sigma-factor involved in cell survival in suboptimal conditions, plays a role in EDL933 proliferation by controlling the production of pectate lyases in Dickeya dadantii 3937, e.g. via negative regulation of pelD promoter activity
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additional information
-
invariant amino acids involved in catalytic function mainly comprised the catalytic residues R275, K244, and R280, and the Ca2+-binding residues D151, D173, and D177 in PelN
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additional information
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the organism is the soft rot pathogen of calla lily growing around Kunming, soft rot is a major disease of calla lily, Zantedeschia spp., and other important crops worldwide. The pectate lyase contributes to the disease by tuber maceration cleaving structural pectic polymers, overview
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additional information
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the enzyme from Xanthomonas campestris ACCC 10048 is a low-temperature-active alkaline pectate lyase
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
de-esterified pectin
4,5-unsaturated oligogalacturonates
PEL can randomly catalyze the apha(1-4) linkages of de-esterified pectin by beta-elimination
-
-
?
esterified pectin
?
94% esterified pectin. 97% of the activity with polygalacturonic acid
-
?
oligogalacturonic acid
?
-
the enzyme acts on polygalacturonic acids and oligogalacturonic acids over digalacturonic acid and better on the larger galacturonic acids until at least DP8
-
?
pectin
unsaturated oligogalacturonides
-
esterified citrus pectin
-
?
pentagalacturonic acid
saturated digalacturonic acid + unsaturated trigalacturonic acid + saturated trigalacturonic acid + unsaturated digalacturonic acid
polygalacturonate
unsaturated trigalacturonate + unsaturated oligogalacturonates
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
major product
-
?
polygalacturonic
?
analysis of polygalacturonic acid degradation products by electrospray ionization-mass spectrometry reveal that the degradation products are unsaturated trigalacturonic acid and unsaturated bigalacturonic acid, which confirms that the enzyme catalyzes a trans-elimination reaction
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-
?
polygalacturonic acid
4,5-unsaturated digalacturonic acid + 4,5-unsaturated trigalacturonic acid + oligogalacturonic acid
polygalacturonic acid
DELTA4,5-unsaturated oligogalacturonides
-
-
?
reduced tetragalacturonic acid
galacturonic acid + reduced trigalacturonic acid
-
-
-
?
tetragalacturonic acid
altered trigalacturonic acid + digalacturonic acid + altered digalacturionic acid + D-galacturonic acid
citrus pectin
?
PelA shows 25% relative activity on citrus pectin compared to polygalacturonate
-
-
?
citrus pectin
?
PelA shows 25% relative activity on citrus pectin compared to polygalacturonate
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-
?
esterified pectin
unsaturated tetragalacturonic acid
-
affinity shows a maximum for intermediate esterified pectins and decreases over a value of 50% of esterification. The best substrate is 29.5% methylated pectin
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-
?
esterified pectin
unsaturated tetragalacturonic acid
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affinity shows a maximum for intermediate esterified pectins and decreases over a value of 50% of esterification. The best substrate is 29.5% methylated pectin
-
-
?
hexagalacturonic acid
?
-
17.2% of the activity with polygalacturonic acid
-
-
?
hexagalacturonic acid
?
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140% of the activity with low molecular weight polygalacturonic acid
-
-
?
oligogalacturonate
unsaturated digalacturonate
-
isoenzyme PelB and pelD show highest activity on hexagalacturonate and tetragalacturonate, respectively. Isoenzyme pelA, pelB and pelL are most active on the octamer
the preferential products formed are unsaturated dimer for isoenzyme PelD, unsaturated trimer for isoenzyme PelB, and unsaturated tetramer for isoenzyme PelI and PelL. For isoenzyme pelA, preferential products are dependent on the size of the oligogalacturonate
?
oligogalacturonate
unsaturated digalacturonate
-
isoenzyme PelB and pelD show highest activity on hexagalacturonate and tetragalacturonate, respectively. Isoenzyme pelA, pelB and pelL are most active on the octamer
the preferential products formed are unsaturated dimer for isoenzyme PelD, unsaturated trimer for isoenzyme PelB, and unsaturated tetramer for isoenzyme PelI and PelL. For isoenzyme pelA, preferential products are dependent on the size of the oligogalacturonate
?
pectate
?
i.e. polygalacturonic acid, cleavage of the pectate alpha-1,4-glycosidic bond by Pel-BL11
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-
?
pectate
?
i.e. polygalacturonic acid, cleavage of the pectate alpha-1,4-glycosidic bond by Pel-BL11
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-
?
pectic acid
oligouronides of heterogeneous size
-
acid soluble
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-
?
pectic acid
oligouronides of heterogeneous size
-
acid soluble
-
-
?
pectic acid amide
?
-
about 15% of activity with acid soluble pectic acid
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-
?
pectic acid amide
?
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about 15% of activity with acid soluble pectic acid
-
-
?
pectin
?
-
low-esterified pectin (30%) is the optimum substrate for the PelA, higher-esterified pectin is hardly cleaved
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-
?
pectin
?
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low-esterified pectin (30%) is the optimum substrate for the PelA, higher-esterified pectin is hardly cleaved
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-
?
pectin
?
-
at about 12% of the activity with acid soluble pectic acid
-
-
?
pectin
?
of methyl esterification degree from 22-89%. Similar activity on polygalacturonic acid and on 89% esterified citrus pectin
-
?
pectin
?
relative degradation rates of citrus pectin with methylation degrees 31%, 63% and 94% is 124%, 73% and 9% compared to polygalacturonic acid
-
?
pectin
?
with degrees of esterification of 31%, 63% and 94% is degraded with 103%, 84% and 46% of the activity with polygalacturonic acid
-
?
pectin
?
of methyl esterification degree from 22-89%. Similar activity on polygalacturonic acid and on 89% esterified citrus pectin
-
?
pectin
?
Bacillus sp. (in: Bacteria) KSM-P15
with degrees of esterification of 31%, 63% and 94% is degraded with 103%, 84% and 46% of the activity with polygalacturonic acid
-
?
pectin
?
Bacillus sp. (in: Bacteria) KSM-P15
relative degradation rates of citrus pectin with methylation degrees 31%, 63% and 94% is 124%, 73% and 9% compared to polygalacturonic acid
-
?
pectin
?
-
at about 12% of the activity with acid soluble pectic acid
-
-
?
pectin
?
-
of methyl esterification degree from 22% to 89%, maximal activity on 22% esterified citrus pectin
-
-
?
pectin
?
-
pectate lyases harness anti beta-elimination chemistry to cleave the alpha-1,4 linkage in the homogalacturonan region of plant cell wall pectin
-
-
?
pectin
?
apple or citrus pectin, activity with pectin is lower than activity with polygalacturonate
-
-
?
pectin
?
-
apple pectin, citrus pectin, as the percentage of methylation in pectin becomes higher, the activities become lower
-
-
?
pectin
?
apple or citrus pectin, activity with pectin is lower than activity with polygalacturonate
-
-
?
pectin
?
-
unlike other isoenzymes, pectate lyase requires partially methyl esterified pectin as substrate
-
-
?
pectin
?
-
better substrate for pectate lyase I than polygalacturonic acid
-
?
pectin
?
80% of the activity with polygalacturonic acid
-
?
pentagalacturonic acid
saturated digalacturonic acid + unsaturated trigalacturonic acid + saturated trigalacturonic acid + unsaturated digalacturonic acid
-
5.9% of the activity with polygalacturonic acid
-
-
?
pentagalacturonic acid
saturated digalacturonic acid + unsaturated trigalacturonic acid + saturated trigalacturonic acid + unsaturated digalacturonic acid
-
-
-
-
?
pentagalacturonic acid
saturated digalacturonic acid + unsaturated trigalacturonic acid + saturated trigalacturonic acid + unsaturated digalacturonic acid
-
215% of the activity with low molecular weight polygalacturonic acid
-
-
?
pentagalacturonic acid
saturated digalacturonic acid + unsaturated trigalacturonic acid + saturated trigalacturonic acid + unsaturated digalacturonic acid
-
-
preferentially split into saturated digalacturonic acid + unsaturated trigalacturonic acid or into saturated trigalacturonic acid + unsaturated digalacturonic acid - at a lower rate it is also split into monogalacturonic acid and unsaturated tetragalacturonic acid
?
polygalacturonate
unsaturated 4,5-digalacturonate + unsaturated 4,5-trigalacturonate
-
-
-
?
polygalacturonate
unsaturated 4,5-digalacturonate + unsaturated 4,5-trigalacturonate
-
-
-
?
polygalacturonate
unsaturated 4,5-digalacturonate + unsaturated 4,5-trigalacturonate + ?
the enzyme is specific toward alpha-1,4-galacturonic acid linkages of galactopolysaccharides
main products
-
?
polygalacturonate
unsaturated 4,5-digalacturonate + unsaturated 4,5-trigalacturonate + ?
the enzyme is specific toward alpha-1,4-galacturonic acid linkages of galactopolysaccharides
main products
-
?
polygalacturonate
unsaturated oligo-galacturonides
-
the enzyme produces unsaturated oligo-galacturonides including unsaturated tri-galacturonic acid and unsaturated bi-galacturonic acid but not unsaturated mono-galacturonic acid
-
-
?
polygalacturonate
unsaturated oligo-galacturonides
-
the enzyme produces unsaturated oligo-galacturonides including unsaturated tri-galacturonic acid and unsaturated bi-galacturonic acid but not unsaturated mono-galacturonic acid
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
Bacillus sp. (in: Bacteria) KSM-P15
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated oligogalacturonides
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
-
-
-
-
?
polygalacturonate
unsaturated tetragalacturonate
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated tetragalacturonate
-
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
-
-
?
polygalacturonate
unsaturated tetragalacturonic acid
-
the enzyme cleaves polygalacturonic acid via a beta-elimination mechanism
-
-
?
polygalacturonate
unsaturated tetragalacturonic acid
-
the enzyme cleaves polygalacturonic acid via a beta-elimination mechanism
-
-
?
polygalacturonic acid
4,5-unsaturated digalacturonic acid + 4,5-unsaturated trigalacturonic acid + oligogalacturonic acid
-
unsaturated di- and trigalacturonic acids are mainly formed as the final products of degradation by Pel SWU
-
?
polygalacturonic acid
4,5-unsaturated digalacturonic acid + 4,5-unsaturated trigalacturonic acid + oligogalacturonic acid
-
unsaturated di- and trigalacturonic acids are mainly formed as the final products of degradation by Pel SWU
-
?
polygalacturonic acid
4,5-unsaturated digalacturonic acid + 4,5-unsaturated trigalacturonic acid + oligogalacturonic acid
-
endo-type reaction
-
?
polygalacturonic acid
4,5-unsaturated digalacturonic acid + 4,5-unsaturated trigalacturonic acid + oligogalacturonic acid
-
endo-type reaction, little action on highly esterified polygalacturonic acid methylglucoside.The enzyme acts on polygalacturonic acids and oligogalacturonic acids over digalacturonic acid and better on the larger galacturonic acids until at least DP8
-
?
polygalacturonic acid
?
Arg235 is an essential catalytic residue
-
-
?
polygalacturonic acid
?
Arg235 is an essential catalytic residue
-
-
?
polygalacturonic acid
?
degradation through an endo-type fashion
-
?
polygalacturonic acid
?
Bacillus sp. (in: Bacteria) KSM-P15
degradation through an endo-type fashion
-
?
polygalacturonic acid
?
the recombinant enzyme shows highest activity on polygalacturonic acid and lower activity on more highly methylated pectin
-
-
?
polygalacturonic acid
?
-
Arg initiates proton abstration during the beta elimination cleavage of polygalacturonic acid
-
?
polygalacturonic acid
?
best substrate
final major end products are dimers, trimers, and tetramers of unsaturated galacturonic acid, PelB does not produce any monomeric GalpA
-
?
polygalacturonic acid
?
enzyme is found to be active on both polygalacturonic acid and citrus pectin as substrates, although it appears to prefer polygalacturonic acid
-
-
?
polygalacturonic acid
?
enzyme shows over ten times higher catalytic efficiency towards polygalacturonic acid than towards citrus pectin
-
-
?
polygalacturonic acid
unsaturated galacturonate
-
-
-
?
polygalacturonic acid
unsaturated oligogalacturonate
-
random attack
-
-
-
polygalacturonic acid
unsaturated oligogalacturonate
-
random attack
a mixture of 4,5-unsaturated oligogalacturonides, approximately molar ratios of 12:74:14 for monomer, dimer, and trimer, respectively
?
polygalacturonic acid
unsaturated oligogalacturonate
Bacillus sp. (in: Bacteria) KSM-P15
-
random attack
a mixture of 4,5-unsaturated oligogalacturonides, approximately molar ratios of 12:74:14 for monomer, dimer, and trimer, respectively
?
polygalacturonic acid
unsaturated oligogalacturonate
-
random attack
-
-
-
polygalacturonic acid
unsaturated oligogalacturonate
-
activity decreases when the methoxyl content of the substrate increases
-
-
?
polygalacturonic acid
unsaturated oligogalacturonate
-
-
the main product appears to be a disaccharide that contains a DELTA4,5-unsaturated galacturonic acid residue
?
polygalacturonic acid
unsaturated oligogalacturonate
-
-
isoenzyme PelA, PelI and PelL release oligogalacturonates of different sizes, isoenzyme PelD, pelB release mostly unsaturated dimer and unsaturated trimer, respectively
?
polygalacturonic acid
unsaturated oligogalacturonate
-
with a low degree of methylation
-
-
?
polygalacturonic acid
unsaturated oligogalacturonate
-
with a low degree of methylation
-
-
?
polygalacturonic acid
unsaturated oligogalacturonate
-
-
isoenzyme PelA, PelI and PelL release oligogalacturonates of different sizes, isoenzyme PelD, pelB release mostly unsaturated dimer and unsaturated trimer, respectively
?
polygalacturonic acid
unsaturated oligogalacturonate
-
endo-cleavage
-
-
?
polygalacturonic acid
unsaturated oligogalacturonate
-
endo-cleavage
wide range of 4,5-unsaturated oligogalacturonates, further depolymerized to unsaturated dimer and trimer
?
polygalacturonic acid
unsaturated oligogalacturonate
-
random attack
-
-
?
polygalacturonic acid
unsaturated oligogalacturonate
-
random attack
higher oligomers are detected in the early stage of degradation, unsaturated monogalacturonic acids and digalacturonic acids are also detected after prolonged degradation
?
polygalacturonic acid
unsaturated oligogalacturonate
-
low molecular weight. High molecular weight polygalacturonic acid is attacked at 46% of the activity with low molecular weight polygalacturonic acid
higher oligomers are detected in the early stage of degradation, unsaturated monogalacturonic acids and digalacturonic acids are also detected after prolonged degradation
?
polygalacturonic acid
unsaturated oligogalacturonate
-
-
end products at 46% saturation: unsaturated digalacturonic acids, unsaturated trigalacturonic acids, saturated monogalacturonic acid + saturated digalacturonic acid + saturated trigalacturonic acid
?
polygalacturonic acid
unsaturated oligogalacturonate + ?
specific substrate, enzyme activity decreases when the methoxyl content of the substrate increases
-
-
?
polygalacturonic acid
unsaturated oligogalacturonate + ?
specific substrate, enzyme activity decreases when the methoxyl content of the substrate increases
-
-
?
polygalacturonic acid
unsaturated oligogalacturonide
-
-
?
polygalacturonic acid
unsaturated oligogalacturonides
-
-
?
polygalacturonic acid
unsaturated oligogalacturonides
-
i.e. pectate, endo-cleavage, the enzyme has a preference for sequences of non-esterified galacturonic acid residues
-
?
tetragalacturonic acid
altered trigalacturonic acid + digalacturonic acid + altered digalacturionic acid + D-galacturonic acid
-
-
only trace amounts of digalacturonic acid
?
tetragalacturonic acid
altered trigalacturonic acid + digalacturonic acid + altered digalacturionic acid + D-galacturonic acid
-
-
-
-
?
tetragalacturonic acid
altered trigalacturonic acid + digalacturonic acid + altered digalacturionic acid + D-galacturonic acid
-
141% of the activity with low molecular weight polygalacturonic acid
-
-
?
trigalacturonate
?
-
enzyme and substrate-binding structures, overview
-
-
?
trigalacturonate
?
-
enzyme and substrate-binding structures, overview
-
-
?
trigalacturonic acid
altered digalacturonic acid + galacturonic acid
-
-
-
?
trigalacturonic acid
altered digalacturonic acid + galacturonic acid
-
-
-
-
?
trigalacturonic acid
altered digalacturonic acid + galacturonic acid
-
3% of the activity with low molecular weight polygalacturonic acid
-
-
?
additional information
?
-
-
in the completed genome of Arabidopsis, there are 26 genes that encode pectate lyase-like proteins. The stability of transcripts of PLLs varies considerably among different genes. Complex regulation of expression of PLLs and involvement of PLLs in some of the hormonal and stress responses. several PLLs are expressed highly in pollen, suggesting a role for these in pollen development and/or function
-
-
-
additional information
?
-
-
PelA efficiently macerates mung bean hypocotyls and potato tuber tissues into single cells
-
-
-
additional information
?
-
-
PelA efficiently macerates mung bean hypocotyls and potato tuber tissues into single cells
-
-
-
additional information
?
-
substrates are 45% methylated pectin or polygalacturonate
-
-
-
additional information
?
-
substrates are 45% methylated pectin or polygalacturonate
-
-
-
additional information
?
-
-
protopectinase-like activity on cotton fibers
-
-
-
additional information
?
-
PelA does not show any activity on mannan, CMC, xylan, glucan, or soluble starch
-
-
-
additional information
?
-
Bacillus sp. (in: Bacteria) KSM-P15
-
protopectinase-like activity on cotton fibers
-
-
-
additional information
?
-
PelA does not show any activity on mannan, CMC, xylan, glucan, or soluble starch
-
-
-
additional information
?
-
-
enzyme production is repressed by glucose
-
-
-
additional information
?
-
-
digalacturonate is not cleaved at an appreciable rate
-
-
-
additional information
?
-
substrates are 45% methylated pectin or polygalacturonate
-
-
-
additional information
?
-
substrates are 45% methylated pectin or polygalacturonate
-
-
-
additional information
?
-
-
the enzyme plays an important role in plant-nematode interactions
-
-
-
additional information
?
-
the enzyme plays an important role in plant-nematode interactions
-
-
-
additional information
?
-
-
the enzyme secreted by the bacterium into the human large intestine cooperatively digests pectic substances, producing mainly 4,5-unsaturated digalacturonic acid with the participation of the pectin methyltransferase
-
?
additional information
?
-
-
the enzyme secreted by the bacterium into the human large intestine cooperatively digests pectic substances, producing mainly 4,5-unsaturated digalacturonic acid with the participation of the pectin methyltransferase
-
?
additional information
?
-
as the external pH increases from 4.0 to 6.0, pectate lyase and other extracellular proteins are secreted and accumulate. Nitrogen assimilation also is required for enzyme secretion at pH 6.0. The ambient pH and the nitrogen source are independent regulatory factors for processes linked to secretion of pectate lyase and virulence of Colletotrichum gloeosporioides
-
?
additional information
?
-
-
the pathogenicity of Colletotrichum gloeosporioides is dependent on its ability to secrete pectate lyase. The host pH in pericarp regulates the secretion. Secretion is detected when the pH reaches 5.8 and the level of secretion increases up to pH 6.5
-
?
additional information
?
-
-
when the fungus is grown at pH 4.0 or 6.0 in the absence of a nitrogen source, neither pelB (encoding pectate lyase) transcription nor pectate lyase secretion is detected. pelB transcription and pectate lyase secretion are both detected when Colletotrichum gloeosporioides is grown at pH 6.0 in the presence of ammonia accumulated from different nitrogen sources. The early accumulation of ammonia induces early pelB expression and pectate lyase secretion. Nit mutants of Colletotrichum gloeosporioides, which cannot utilize KNO3 as a nitrogen source, do not secrete ammonia, alkalinize the medium, or secrete pectate lyase. If Nit mutants are grown at pH 6.0 in the presence of glutamate, then pectate lyase secretion is induced
-
-
-
additional information
?
-
-
optimization of chemical and physical parameters affecting the activity of pectate lyase
-
-
-
additional information
?
-
-
pectate lyase E is most effective in causing maceration and inducing electrolyte loss and cell death in potato tuber tissue
-
-
-
additional information
?
-
-
colonization of plant tissues by the phytopathogen Erwinia chrysanthemi E16 is aided by the activities of the pectate lyase isoenzymes, which depolymerize the polygalacturonic acid component of the plant cell walls
-
?
additional information
?
-
-
pectate lyase A is a virulence factor for soft rot diseases in plants
-
?
additional information
?
-
-
pectate lyase A is a virulence factor secreted by the plant pathogenic bacterium Erwinia chrysanthemi
-
?
additional information
?
-
-
pectate lyase E is most effective in causing maceration and inducing electrolyte loss and cell death in potato tuber tissue
-
-
-
additional information
?
-
-
pectate lyase A is a virulence factor for soft rot diseases in plants
-
?
additional information
?
-
-
pectate lyase A is a virulence factor secreted by the plant pathogenic bacterium Erwinia chrysanthemi
-
?
additional information
?
-
-
colonization of plant tissues by the phytopathogen Erwinia chrysanthemi E16 is aided by the activities of the pectate lyase isoenzymes, which depolymerize the polygalacturonic acid component of the plant cell walls
-
?
additional information
?
-
-
PelN acts synergistically with other pectate lyases in the organism, activity comparisons, overview
-
-
-
additional information
?
-
-
the Gr-PEL2 protein is capable of inducing profound changes in the plant morphology, not related to tissue maceration or soft rot
-
-
-
additional information
?
-
substrates are 45% methylated pectin or polygalacturonate
-
-
-
additional information
?
-
-
substrates are 45% methylated pectin or polygalacturonate
-
-
-
additional information
?
-
substrates are highly methylated pectin and polygalacturonic acid, substrate specificity of PelA, overview
-
-
-
additional information
?
-
substrates are highly methylated pectin and polygalacturonic acid, substrate specificity of PelA, overview
-
-
-
additional information
?
-
-
substrates are highly methylated pectin and polygalacturonic acid, substrate specificity of PelA, overview
-
-
-
additional information
?
-
substrates are highly methylated pectin and polygalacturonic acid, substrate specificity of PelB, overview
-
-
-
additional information
?
-
substrates are highly methylated pectin and polygalacturonic acid, substrate specificity of PelB, overview
-
-
-
additional information
?
-
-
substrates are highly methylated pectin and polygalacturonic acid, substrate specificity of PelB, overview
-
-
-
additional information
?
-
substrates are highly methylated pectin and polygalacturonic acid, substrate specificity of PelA, overview
-
-
-
additional information
?
-
substrates are highly methylated pectin and polygalacturonic acid, substrate specificity of PelA, overview
-
-
-
additional information
?
-
substrates are highly methylated pectin and polygalacturonic acid, substrate specificity of PelB, overview
-
-
-
additional information
?
-
substrates are highly methylated pectin and polygalacturonic acid, substrate specificity of PelB, overview
-
-
-
additional information
?
-
-
no activity with digalacturonic acid
-
-
-
additional information
?
-
PelN exhibits relatively high activity on methylated substrates. On pectin with relatively low degree (20-34%) of methylation, the remaining specific activity of PelN is approximately 100% of that on polygalacturonic acid. Highly methylated pectin (55-70%) results in slight inhibition of the PelN activity to 74%
-
-
-
additional information
?
-
PelN exhibits relatively high activity on methylated substrates. On pectin with relatively low degree (20-34%) of methylation, the remaining specific activity of PelN is approximately 100% of that on polygalacturonic acid. Highly methylated pectin (55-70%) results in slight inhibition of the PelN activity to 74%
-
-
-
additional information
?
-
-
the pectate lyase isoenzyme PelS appears to alter the final symptoms in infected cucumber cotyledons without contributing to pathogenicity or altering host range
-
-
-
additional information
?
-
-
macerating activity on Ganpi bark, carrot, radish and sweet potato
-
-
-
additional information
?
-
-
macerating activity on potato tissue and Ganpi bark
-
-
-
additional information
?
-
-
digalacturonic acid and trigalacturonic acid are not good substrates
-
-
-
additional information
?
-
-
no macerating activity on Gampi bark, carrot, potato, cabbage and radish
-
-
-
additional information
?
-
the enzyme is involved in degradation of the pectate portion of the primary plant cell wall
-
?
additional information
?
-
-
the enzyme is involved in degradation of the pectate portion of the primary plant cell wall
-
?
additional information
?
-
PelB is an endo-acting lyase and shows high cleavage capability on a broad range of substrates of natural methylated pectin, substrate specificity, overview
-
-
-
additional information
?
-
-
the enzyme activity against polygalacturonic acid as 100%, r-PL D exhibits 91.7%, 47.3%, and 6.5% of the activity when pectin is methyl-esterified 34%, 70%, and 85%, respectively
-
-
-
additional information
?
-
-
the enzyme activity against polygalacturonic acid as 100%, r-PL D exhibits 91.7%, 47.3%, and 6.5% of the activity when pectin is methyl-esterified 34%, 70%, and 85%, respectively
-
-
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
-
in the completed genome of Arabidopsis, there are 26 genes that encode pectate lyase-like proteins. The stability of transcripts of PLLs varies considerably among different genes. Complex regulation of expression of PLLs and involvement of PLLs in some of the hormonal and stress responses. several PLLs are expressed highly in pollen, suggesting a role for these in pollen development and/or function
-
-
-
additional information
?
-
-
enzyme production is repressed by glucose
-
-
-
additional information
?
-
-
the enzyme plays an important role in plant-nematode interactions
-
-
-
additional information
?
-
Q33CQ4
the enzyme plays an important role in plant-nematode interactions
-
-
-
additional information
?
-
-
the enzyme secreted by the bacterium into the human large intestine cooperatively digests pectic substances, producing mainly 4,5-unsaturated digalacturonic acid with the participation of the pectin methyltransferase
-
?
additional information
?
-
-
the enzyme secreted by the bacterium into the human large intestine cooperatively digests pectic substances, producing mainly 4,5-unsaturated digalacturonic acid with the participation of the pectin methyltransferase
-
?
additional information
?
-
Q8J254
as the external pH increases from 4.0 to 6.0, pectate lyase and other extracellular proteins are secreted and accumulate. Nitrogen assimilation also is required for enzyme secretion at pH 6.0. The ambient pH and the nitrogen source are independent regulatory factors for processes linked to secretion of pectate lyase and virulence of Colletotrichum gloeosporioides
-
?
additional information
?
-
-
the pathogenicity of Colletotrichum gloeosporioides is dependent on its ability to secrete pectate lyase. The host pH in pericarp regulates the secretion. Secretion is detected when the pH reaches 5.8 and the level of secretion increases up to pH 6.5
-
?
additional information
?
-
-
when the fungus is grown at pH 4.0 or 6.0 in the absence of a nitrogen source, neither pelB (encoding pectate lyase) transcription nor pectate lyase secretion is detected. pelB transcription and pectate lyase secretion are both detected when Colletotrichum gloeosporioides is grown at pH 6.0 in the presence of ammonia accumulated from different nitrogen sources. The early accumulation of ammonia induces early pelB expression and pectate lyase secretion. Nit mutants of Colletotrichum gloeosporioides, which cannot utilize KNO3 as a nitrogen source, do not secrete ammonia, alkalinize the medium, or secrete pectate lyase. If Nit mutants are grown at pH 6.0 in the presence of glutamate, then pectate lyase secretion is induced
-
-
-
additional information
?
-
-
optimization of chemical and physical parameters affecting the activity of pectate lyase
-
-
-
additional information
?
-
-
colonization of plant tissues by the phytopathogen Erwinia chrysanthemi E16 is aided by the activities of the pectate lyase isoenzymes, which depolymerize the polygalacturonic acid component of the plant cell walls
-
?
additional information
?
-
-
pectate lyase A is a virulence factor for soft rot diseases in plants
-
?
additional information
?
-
-
pectate lyase A is a virulence factor secreted by the plant pathogenic bacterium Erwinia chrysanthemi
-
?
additional information
?
-
-
pectate lyase A is a virulence factor for soft rot diseases in plants
-
?
additional information
?
-
-
pectate lyase A is a virulence factor secreted by the plant pathogenic bacterium Erwinia chrysanthemi
-
?
additional information
?
-
-
colonization of plant tissues by the phytopathogen Erwinia chrysanthemi E16 is aided by the activities of the pectate lyase isoenzymes, which depolymerize the polygalacturonic acid component of the plant cell walls
-
?
additional information
?
-
-
the Gr-PEL2 protein is capable of inducing profound changes in the plant morphology, not related to tissue maceration or soft rot
-
-
-
additional information
?
-
-
the pectate lyase isoenzyme PelS appears to alter the final symptoms in infected cucumber cotyledons without contributing to pathogenicity or altering host range
-
-
-
additional information
?
-
Q9WYR4
the enzyme is involved in degradation of the pectate portion of the primary plant cell wall
-
?
additional information
?
-
-
the enzyme is involved in degradation of the pectate portion of the primary plant cell wall
-
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ba2+
Ca2+
Co2+
Cu2+
Fe2+
K+
Mg2+
Mn2+
Na+
Sr2+
Zn2+
additional information
Ba2+
the enzyme is activated slightly in the presence of BaCl2
Ca2+
strong sigmoidal CaCl2 concentration dependent relation. Optimal catalysis at 0.5-1.0 mM Ca2+
Ca2+
required for activity on pectic substrates, maximal activity at 0.5-0.75 mM CaCl2. Only 9% of maximal activity at 10 mM CaCl2
Ca2+
Ca2+ is not required for activity on pectic substrates
Ca2+
-
the enzyme in the absence of substrate binds a single calcium ion, two additional calcium ions bind between enzyme and substrate carboxylates occupying the +1 subsite in the Michaelis complex
Ca2+
required, activates the recombinant enzyme from Pichia pastoris by 26%
Ca2+
-
optimal activity in presence of 2.0-4.0 mM Ca2+. No activity when Ca2+ is replaced with Co2+, Cu2+, Ba2+, Mg2+, Mn2+, Ni2+, Sr2+ or Zn2+
Ca2+
-
both pectate lyase I and II require 0.2 mM Ca2+ for maximal activity
Ca2+
-
absolute requirement, maximal activity of recombinantly expressed full-length enzyme at 0.05 mM, maximal activity of recombinantly expressed catalytic module CM9-1 at 0.02 mM, maximal activity of recombinantly expressed catalytic module CM9-2 at 0.1 mM
Ca2+
-
the Ca2+ site consists primarily of beta-turns and beta-strands. The Ca2+ affinity for the enzyme is weak. Kd: 0.132 mM at pH 9.5, 1.09 mM at pH 11.2 and 5.84 mM at pH 4.5. Enzymatic activity at pH 4.5 is greatest at 30 mM Ca2+
Ca2+
-
the enzyme has a single high affinity calcium-binding site. A second Ca2+ binds between enzyme and substrate in the Michaelis complex
Ca2+
optimum Ca2+ concentration at 0.5 mM; optimum concentration at 0.6 mM
Ca2+
-
optimum concentration at 1.0 mM, Ca2+ cannot be replaced by Ba2+, Be2+, Sr2+, Mg2+, and monovalent cations for Pel activity
Ca2+
-
enzyme from Alpine strain A15 completely loses activity in absence of Ca2+; enzyme from Siberian strain AG25 completely loses activity in absence of Ca2+
Ca2+
-
required, can be replaced by Mn2+ or Mg2+. Optimal activity at 0.7 mM. Additive effect when any two metal ions (Mg2+, Ca2+, Mn2+) are present together
Ca2+
activates optimally at 0-2.5 mM; activates optimally at 0-2.5 mM
Ca2+
required, 7.3fold activation at 0.5 mM, 4.4fold at 1 mM, Ca2+-binding residues are D151, D173, and D177 in PelN
Ca2+
-
0.5 mM, 7fold activation of pectate lyase I, 4fold activation of pectate lyase II
Ca2+
-
absolute requirement for Ca2+for pectin degradation, no other divalent cation (Mg2+, Mn2+, Ba2+, Cu2+, Zn2+ or Co2+) can substitute for Ca2+, pectate lyase activity is undetectable without Ca2+ and the maximum activity is at 0.75 mm CaCl2, while enzymatic activity decreases at higher concentrations of Ca2+
Ca2+
-
required, optimal concentration varies with levels of the substrate
Mg2+
-
can substitute for Ca2+ in activation. Optimal activity at 0.7 mM. Additive effect when any two metal ions (Mg2+, Ca2+, Mn2+) are present together
Mn2+
-
can substitute for Ca2+ in activation. Optimal activity at 0.7 mM. Additive effect when any two metal ions (Mg2+, Ca2+, Mn2+) are present together
additional information
Fe2+ and Cu2+ do not significantly affect the activity of Pel-66
additional information
no or poor effect on the recombinant enzyme from Pichia pastoris by Sr2+, K+, and Li+
additional information
-
no activation by Ca2+, Co2+, Cu2+, Mg2+, Mn2+, Ni2+, Zn2+, or Ba2+,
additional information
Fe2+ and Ni2+ do not significantly affect the activity of Pel-90
additional information
-
Fe2+ and Ni2+ do not significantly affect the activity of Pel-90
additional information
-
divalent cations are required for maximum activity
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ascorbic acid
-
48% loss of activity at 0.1 mM, complete inactivation at 1.0 mM
calcium-alginate
-
calcium-alginate concentration levels higher or lower 38.5 units/ml result in reduced enzyme activity
-
2-mercaptoethanol
-
29% loss of activity at 1 mM, 67% loss of activity at 5 mM
Ba2+
causes a severe loss of activity, 88% inhibtion at 0.5 mM, 97% at 1 mM
Ca2+
Ca2+ does not increase but instead inhibits the activity of PelA, 41% residual activity at 1 mM
EDTA
1 mM, in 50 mM Tris-HCl buffer, pH 7.5, 10 min at 30°C, complete inhibition, activity recovered by addition of 0.1 mM CaCl2
EDTA
1 mM, pH 7.5, 10 min at 30°C, activity is completely abolished, fully recovered by adding 0.8 mM CaCl2
EDTA
PelA is sensitive to 10 mM EDTA with 39% activity retained
EDTA
-
1 mM, enzyme from Alpine strain A15 loses 67% of initial activity, complete inactivation at 10 mM; 1 mM, enzyme from Siberian strain AG25 loses 85% of initial activity, complete inactivation at 10 mM
EDTA
-
inhibits activity with polygalacturonate, no inhibition of the ability to cleave protopectin of Boehmeria nivea
EDTA
3 mM, complete inhibition. Lyase activity can be restored by further addition of 5 mM CaCl2
epicatechin
-
epicatechin may be involved in the resistance of unripe avocado fruits by inhibiting the pectate lyase activity of Colletotrichum gloeosporoides