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Information on EC 4.2.2.9 - pectate disaccharide-lyase
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4.2.2.9 pectate disaccharide-lyaseIUBMB Comments
The enzyme catalyses the eliminative cleavage of an unsaturated disaccharide from the reducing end of homogalacturonan (the backbone of smooth regions of pectate, also known as de-esterified pectin).
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Word Map
- 4.2.2.9
- pectin
- polygalacturonic
-
pectinolytic
- endopolygalacturonase
-
erwinia
- polygalacturonases
- oligogalacturonates
- chrysanthemi
-
macer
-
digalacturonic
- exopgs
-
endo-pectate
- tubingensis
- trigalacturonate
-
lycopersici
-
soft-rot
- pectinesterase
- pectinases
-
methyl-esterified
-
exo-poly-alpha-d-galacturonosidase
- industry
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Reaction Schemes
Synonyms
exo-PATE, exo-pectate lyase, exo-PGL, exocleaving pectate lyase, exopectate lyase, exopectate lyase W, exopectate pectate lyase, exopectic acid transeliminase, ExoPL, exopolygalacturonase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
exo-PATE
-
-
-
-
exo-PGL
-
-
-
-
exocleaving pectate lyase
exopectate lyase
exopectate pectate lyase
exopectic acid transeliminase
-
-
-
-
ExoPL
-
-
-
-
Exopolygalacturonate lyase
-
-
-
-
lyase, exopolygalacturonate
-
-
-
-
PelL
-
-
-
-
PelW
PelX
poly(1,4-alpha-D-galacturonide) exo-lyase
-
-
-
-
exopectate lyase
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(1,4-alpha-D-galacturonosyl)n = (1,4-alpha-D-galacturonosyl)n-2 + 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate
(1,4-alpha-D-galacturonosyl)n = (1,4-alpha-D-galacturonosyl)n-2 + 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate
trans-elimination mechanism
Clostridium multifermentans
-
(1,4-alpha-D-galacturonosyl)n = (1,4-alpha-D-galacturonosyl)n-2 + 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
elimination
elimination
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
(1->4)-alpha-D-galacturonan reducing-end-disaccharide-lyase
The enzyme catalyses the eliminative cleavage of an unsaturated disaccharide from the reducing end of homogalacturonan (the backbone of smooth regions of pectate, also known as de-esterified pectin).
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CAS REGISTRY NUMBER
COMMENTARY
37290-87-2
-
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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
1-methyl-di-D-galacturonate
?
-
alpha-(1-4)-linked, 36% of the activity with di-D-galacturonate
-
?
2-methyl-di-D-galacturonate
?
-
alpha-(1-4)-linked, 35% of the activity with di-D-galacturonate
-
?
2-methyl-tri-D-galacturonate
?
-
alpha-(1-4)-linked, 19% of the activity with tri-D-galacturonate or 1-methyl-tri-D-galacturonate
-
?
DELTA4,5-unsaturated tri-D-galacturonate
?
-
alpha-(1-4)-linked, low activity with PelX
-
?
heptagalacturonate
?
better substrate than polygalacturonate
-
-
?
1-methyl-tri-D-galacturonate
?
-
best substrate, alpha-(1-4)-linked
-
?
3-methyl-tri-D-galacturonate
?
-
alpha-(1-4)-linked, 18% of the activity with tri-D-galacturonate or 1-methyl-tri-D-galacturonate
-
?
3-methyl-tri-D-galacturonate
?
-
poor substrate only for PelW, not for PelX
-
?
hexagalacturonic acid
?
better substrate than polygalacturonate
-
-
?
hexagalacturonic acid
?
-
51% of the activity with low molecular polygalacturonic acid
-
-
?
pectic acid
4,5-unsaturated digalacturonic acid
-
acid-soluble pectic acid and acid-insoluble pectic acid
-
-
-
pectic acid
4,5-unsaturated digalacturonic acid
-
acid-soluble pectic acid and acid-insoluble pectic acid
-
-
-
pentagalacturonic acid
?
better substrate than polygalacturonate
-
-
?
pentagalacturonic acid
?
-
60% of the activity with low molecular polygalacturonic acid
-
-
?
polygalacturonate
unsaturated digalacturonate
Clostridium multifermentans
-
-
the major end product is O-(4-deoxy-beta-L-threo-hexopyranos-4-enyluronic acid)-(1,4)-D-galacturonic acid
?
polygalacturonate
unsaturated digalacturonate
Clostridium multifermentans
-
-
plus one molecule of digalacturonate originating from the nonreducing end of the chain
?
polygalacturonate
unsaturated digalacturonate
-
-
4,5-unsaturated digalacturonic acid
?
polygalacturonate
unsaturated digalacturonate
-
low molecular polygalacturonic acid, very low activity with high molecular polygalacturonic acid
-
?
tetragalacturonic acid
?
maximal activity, better substrate than polygalacturonate
-
-
-
tetragalacturonic acid
?
-
maximal activity, better substrate than polygalacturonate
-
-
?
tetragalacturonic acid
?
-
maximal activity, better substrate than polygalacturonate
-
-
?
tetragalacturonic acid
?
-
52% of the activity with low molecular polygalacturonic acid
-
-
?
tri-D-galacturonate
?
-
alpha-(1-4)-linked, best substrate for both enzyme types
-
?
trigalacturonic acid
?
-
248% of the activity with low molecular polygalacturonic acid
-
-
?
additional information
?
-
Clostridium multifermentans
-
no activity with pectin of high methoxyl content
-
-
-
additional information
?
-
-
substrate specificity, overview, no activity for both enzyme types with monomethyl-esterified digalacturonate substrates and with 2-methyl-tri-G-galacturonate
-
?
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NATURAL SUBSTRATE
NATURAL 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
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Co2+
Fe2+
activates, 85% of maximal activity in 0.1 M TES, pH 7.4, 0.1 mM Fe2+
Mg2+
Mn2+
Na+
Sr2+
Ca2+
Clostridium multifermentans
-
greatest stimulation of divalent cations tested, Km: 0.06 mM
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
PelN
presence of PelN has an synergistic effect on PelX activity
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
Clostridium multifermentans
-
Km for polygalacturonate is 0.114% on the basis of dry, ash-free polygalacturonic acid, in presence of 0.5 mM CaCl2
-
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
1.311
-
fractionated enzyme in supernatant fluid, no activity in crude cell extract
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 8.5
Clostridium multifermentans
-
pH 5: no activity, pH 6.0: 15% of maximal activity, pH 7.0: 40% of maximal activity, pH 8.5: maximal activity
7 - 9
Clostridium multifermentans
-
pH 7: about 40% of maximal activity, pH 9: about 85% of maximal activity
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
2 different enzyme types: exopolygalacturonate lyase X, i.e. Pel X, and exopectate lyase W, i.e. PelW
-
-
brenda
gene pelW; i.e. Erwinia chrysanthemi, gene pelW; i.e. Erwinia chrysanthemi, gene pelW
UniProt
brenda
gene pelW; i.e. Erwinia chrysanthemi, gene pelW; i.e. Erwinia chrysanthemi, gene pelW
UniProt
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
Show AA Sequence and Transmembrane Helices (178 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6
Clostridium multifermentans
-
38°C, most stable at
34111
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
45
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
Ca2+ stablizes
Mn2+ stablizes
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PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
ultrafiltration and three-step chromatographic procedures, Sephacryl S-100 column, DEAE-Sepharose ion-exchange column, Sephadex G-50 column chromatography
-
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
industry
-
degumming and retting of fiber crops and pre-treatment of pectic waste water from fruit juice industries
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Shevchik, V.E.; Condemine, G.; Robert-Baudouy, J.; Hugouvieux-Cotte-Pattat, N.
The exopolygalacturonate lyase PelW and the oligogalacturonate lyase Ogl, two cytoplasmic enzymes of pectin catabolism in Erwinia chrysanthemi 3937
J. Bacteriol.
181
3912-3919
1999
Dickeya chrysanthemi, Dickeya chrysanthemi 3937
brenda
Macmillan, J.D.; Phaff, H.J.
Exopolygalacturonate lyase from Clostridium multifermentans. II. Further purification and exopolygalacturonate lyase and pectinesterase from Clostridium multifermentans
Methods Enzymol.
8
632-635
1966
Clostridium multifermentans
-
brenda
Miller, L.; Macmillan, J.D.
Mode of action of pectic enzymes. II. Further purification of exopolygalacturonate lyase and pectinesterase from Clostridium multifermentans
J. Bacteriol.
102
72-78
1970
Clostridium multifermentans
brenda
Macmillan, J.D.; Vaughn, R.H.
Purification and properties of a polygalacturonic acid-trans-eliminase produced by Clostridium multifermentans
Biochemistry
3
564-572
1964
Clostridium multifermentans
brenda
Sato, M.; Kaji, A.
Further properties of the new type of exopolygalacturonate lyase from Streptomyces nitrosporeus
Agric. Biol. Chem.
43
1547-1551
1979
Streptomyces nitrosporeus
-
brenda
Shevchik, V.; Scott, M.; Mayans, O.; Jenkins, J.
Crystallization and preliminary X-ray analysis of a member of a new family of pectate lyases, PeIL from Erwinia chrysanthemi
Acta Crystallogr. Sect. D
54
419-422
1998
Dickeya chrysanthemi 3937, Dickeya chrysanthemi
brenda
Sato, M.; Kaji, A.
Exopolygalacturonate lyase produced by Streptomyces massasporeus
Agric. Biol. Chem.
44
717-721
1980
Streptomyces massasporeus
-
brenda
Hatanaka, C.; Ozawa, J.
Exopectic acid transeliminase of an Erwinia
Agric. Biol. Chem.
36
2307-2313
1972
Erwinia sp., Erwinia sp. W2
-
brenda
Hatanaka, C.; Ozawa, J.
Effect of metal ions on activity of exopectic acid transeliminase of Erwinia sp.
Agric. Biol. Chem.
37
593-597
1973
Erwinia sp.
-
brenda
Shevchik, V.E.; Kester, H.C.M.; Benen, J.A.E.; Visser, J.; Robert-Baudouy, J.; Hugouvieux-Cotte-Pattat, N.
Characterization of the exopolygalacturonate lyase PelX of Erwinia chrysanthemi 3937
J. Bacteriol.
181
1652-1663
1999
Dickeya chrysanthemi, Dickeya chrysanthemi (Q9Z5P8), Dickeya chrysanthemi 3937 (Q9Z5P8)
brenda
Ikeda, S.; Kegoya, Y.; Hatanaka, C.
Effect of chelating agents on exopolygalacturonate lyase of Erwinia carotovora subsp. carotovora
Agric. Biol. Chem.
48
2777-2782
1984
Pectobacterium carotovorum
-
brenda
Kegoya, Y.; Setoguchi, M.; Yokohiki, K.; Hatanaka, C.
Affinity chromatography of exopolygalactururonate lyase from Erwinia carotovora subsp. carotovora
Agric. Biol. Chem.
48
1055-1060
1984
Pectobacterium carotovorum
-
brenda
Kester, H.C.M.; Magaud, D.; Roy, C.; Anker, D.; Doutheau, A.; Shevchik, V.; Hugouvieux-Cotte-Pattat, N.; Benen, J.A.E.; Visser, J.
Performance of selected microbial pectinases on synthetic monomethyl-esterified di- and trigalacturonates
J. Biol. Chem.
274
37053-37059
1999
Aspergillus tubingensis, Dickeya chrysanthemi
brenda
Duskova, D.; Marounek, M.
Fermentation of pectin and glucose, and activity of pectin-degrading enzymes in the rumen bacterium Lachnospira multiparus
Lett. Appl. Microbiol.
33
159-163
2001
Lachnospira multipara
brenda
Celestino, S.M.; Maria de Freitas, S.; Javier Medrano, F.; Valle de Sousa, M.; Filho, E.X.
Purification and characterization of a novel pectinase from Acrophialophora nainiana with emphasis on its physicochemical properties
J. Biotechnol.
123
33-42
2006
Acrophialophora nainiana
brenda
Hassan, S.; Shevchik, V.E.; Robert, X.; Hugouvieux-Cotte-Pattat, N.
PelN is a new pectate lyase of Dickeya dadantii with unusual characteristics
J. Bacteriol.
195
2197-2206
2013
Dickeya dadantii, Dickeya dadantii (E0SDR9), Dickeya dadantii (Q05526), Dickeya dadantii 3937 (E0SDR9), Dickeya dadantii 3937 (Q05526)
brenda
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