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Information on EC 4.2.2.2 - pectate lyase and Organism(s) Dickeya chrysanthemi and UniProt Accession P0C1A2
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4.2.2.2 pectate lyaseIUBMB Comments
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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Word Map
- 4.2.2.2
- erwinia
- chrysanthemi
- lyases
- polygalacturonase
- carotovora
- cellulase
-
macer
-
pectinolytic
-
phytopathogenic
-
soft-rotting
- pectinases
- atroseptica
- homogalacturonan
- polypectate
-
wall-degrading
- pectinesterase
-
textile
-
methylesterase
-
degumming
-
soften
- ramie
- xylanase
-
beta-helix
-
alkaliphilic
- oligogalacturonates
-
4,5-unsaturated
-
enterobacterium
- viridiflava
- digalacturonate
- pectobacterium
- rhamnogalacturonan
-
pectin-degrading
- dickeya
- harpins
- plb
-
plant-parasitic
- dadantii
- gloeosporioides
-
de-esterified
-
bioscouring
- agriculture
- food industry
- biotechnology
- degradation
- industry
-
subventral
- environmental protection
- molecular biology
The taxonomic range for the selected organisms is: Dickeya chrysanthemi
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
pectate lyase, polygalacturonate lyase, pectate lyase c, pectate lyase a, alkaline pectate lyase, pectate lyase b, pel-2, alkaline polygalacturonate lyase, pel9a, pel168, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
alpha-1,4-D-endopolygalacturonic acid lyase
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-
-
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EC 4.2.99.3
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-
-
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endo-alpha-1,4-polygalacturonic acid lyase
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-
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endogalacturonate transeliminase
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-
-
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endopectin methyltranseliminase
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-
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lyase, pectate
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-
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pectate transeliminase
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-
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pectic acid lyase
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-
-
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pectic acid transeliminase
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-
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-
pectic lyase
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-
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PelA
pelC
PelI
PGA lyase
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-
-
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Pla
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-
-
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PLB
PLC
poly(1,4-alpha-D-galacturonide) lyase
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-
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polygalacturonate lyase
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-
-
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polygalacturonic acid lyase
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-
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polygalacturonic transeliminase
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-
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PPase-N
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-
-
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PLB
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-
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PLC
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
elimination
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-
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PATHWAY SOURCE
PATHWAYS
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).
CAS REGISTRY NUMBER
COMMENTARY
9015-75-2
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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
polygalacturonate
unsaturated oligogalacturonides
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
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-
?
oligogalacturonate
unsaturated digalacturonate
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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
?
polygalacturonate
unsaturated oligogalacturonides
pectate lyase cleaves the alpha-1,4 glycosidic bonds of polygalacturonate via a beta-elimination reaction
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-
?
polygalacturonic acid
?
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Arg initiates proton abstration during the beta elimination cleavage of polygalacturonic acid
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?
polygalacturonic acid
unsaturated oligogalacturonate
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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
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with a low degree of methylation
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-
?
additional information
?
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pectate lyase E is most effective in causing maceration and inducing electrolyte loss and cell death in potato tuber tissue
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?
additional information
?
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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
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?
additional information
?
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pectate lyase A is a virulence factor for soft rot diseases in plants
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?
additional information
?
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pectate lyase A is a virulence factor secreted by the plant pathogenic bacterium Erwinia chrysanthemi
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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
additional information
?
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-
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
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?
additional information
?
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pectate lyase A is a virulence factor for soft rot diseases in plants
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?
additional information
?
-
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pectate lyase A is a virulence factor secreted by the plant pathogenic bacterium Erwinia chrysanthemi
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Ca2+
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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+
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the enzyme has a single high affinity calcium-binding site. A second Ca2+ binds between enzyme and substrate in the Michaelis complex
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Mn2+
weakly inhibits PelA activity at 1 mM
Sr2+
weakly inhibits PelA activity at 1 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
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Km-value for lime pectin with 75% methyl esterification: 6.3 mg/ml for wild-type enzyme, 7.8 mg/ml for mutant enzyme D154E, 14.8 mg/ml for mutant enzyme D154N, at 30°C and pH 8.5
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.5
8.8
9.2
8.5
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wild-type enzyme, mutant enzyme R236K and mutant enzyme D154E, lime pectin as substrate
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
55
60
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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the bacterium secretes four pectate lyases: PLa, PLb, PLc and PLe
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
42500
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of PelI is solved to 1.45 A resolution. It consists of an N-terminal domain harboring a fibronectin type III fold linked to a catalytic domain displaying a parallel beta-helix topology. The N-terminal domain is located away from the active site and is not involved in the catalytic process. The structure of PelI in complex with its substrate, a tetragalacturonate, is solved to 2.3 A resolution. The sugar binds from subsites -2 to +2 in one monomer of the asymmetric unit, although it lies on subsites -1 to +3 in the other. These two Michaelis complexes are consistent with the dual mode of bond cleavage in this substrate. The bound sugar adopts a mixed 21 and 31 helical conformation similar to that reported in inactive mutants from families PL-1 and PL-10
crystallographic analysis of 11 enzyme-Ca2+ complexes formed at pH 4.5, 9.5 and 11.2 under varying Ca2+ concentrations, solved and refined at a resolution of 2.2 A
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hanging-drop vapor-diffusion method, crystal structure of the PelA T1.5 mutant solved to 1.6 and 2.9 A resolution. Four residues in the T1.5 loop region of PelA are mutated (N215S, T217S, S219G and A220S) to match the structurally analogous T1.5 loop of PelE
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hanging-drop vapour-diffusion method, unit-cell parameters a = 61.6 A, b = 70.7 A, c = 73.4 A, beta = 112.8°. Crystals diffract to 1.45 A using synchrotron radiation
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oligosaccharide substrate alpha-D-GalpA-((1-4)-alpha-D-GalpA)3-(1-4)-D-GalpA trapped in crystals by using the inactive R218K mutant. Crystals of mutant enzyme R218K are isomorphous with wild-type PelC crystals and belong to space group P2(1)2(1)2(1) with unit cell parameters of a = 72.14 A, b = 78.32 A and c = 94.43 A
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sitting-drop vapour-diffusion method, two crystal forms: monoclinic C2 to 1.8 A and rhombohedral R3 to 21 A
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vapour-diffusion techniques in presence of polyethylene glycol, recombinant enzyme expressed in Escherichia coli
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D154E
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mutant enzyme with 44% of the activity of the wild-type enzyme, the Km-value for the substrate lime pectin (with 75% methyl esterification) is 1.2fold higher than the Km-value of the wild-type enzyme
D154N
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mutant enzyme with 44% of the activity of the wild-type enzyme, the Km-value for the substrate lime pectin (with 75% methyl esterification) is 2.3fold higher than the Km-value of the wild-type enzyme. The pH-optimum is higher than that of the wild-type enzyme
K249R
mutant shows 40-60% of wild-type activity. At a higher Ca2+ concentration in the substrate medium, enzymatic activities of K249R and R252K mutants are less affected
N215S/T217S/S219G/A220S
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the four residues in the T1.5 loop region of PelA are mutated to match the structurally analogous T1.5 loop of PelE. Mutant enzyme shows a conformational change in the T1.5 loop from PelA conformation to that observed in pelE. The pH-optimum of the mutant enzyme is identical to that of PelA, but the T1.5 mutant has an increased specific activity that is comparable to that of PelE
R218K
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inactive mutant enzyme R218K. Crystals of mutant enzyme R218K are isomorphous with wild-type PelC crystals and belong to space group P2(1)2(1)2(1) with unit cell parameters of a = 72.14 A, b = 78.32 A and c = 94.43 A
R252K
mutant shows 6-9% of wild-type activity. At a higher Ca2+ concentration in the substrate medium, enzymatic activities of K249R and R252K mutants are less affected
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
-
half life: 11 min for isoenzyme PelA, 4 min for isoenzyme PelD, 2 min for isoenzyme PelE
60
additional information
-
thermal denaturation is not reversible. The enzyme has its maximal thermal stability at pH 5, CD-monitored thermal denaturation
60
-
half-life: 20-30 min for isoenzyme PelB and PelC, isoenzymes PelA, PelD and PelE loses more than 80% of activity after 2 min
60
-
10 min, 50% loss of activity in absence of cations, 10% loss of activity in presence of Mn2+, Ca2+ or polygalacturonic acid
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
pectate lyase B, C and E are denatured by guanidine hydrochloride with transition midpoint concentrations of 1.3 mM, 1.1 mM and 1.8 mM
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
pectate lyase A, pectate lyase B, pectate lyase C and pectate lyase E, expression in Escherichia coli
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
after complete unfolding in 6 M guanidine-HCl and removal of the denaturant by dialysis, the enzymatic activity of pelC is regained and is identical to that of freshly purified enzyme. Thermal denaturation is not reversible
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ried, J.L.; Collmer, A.
Comparison of pectic enzymes produced by Erwinia chrysanthemi, Erwinia carotovora subsp. carotovora, and Erwinia carotovora subsp. atroseptica
Appl. Environ. Microbiol.
52
305-310
1986
Pectobacterium carotovorum, Dickeya chrysanthemi
Barras, F.; Thurn, K.K.; Chatterjee, A.K.
Resolution of four pectate lyase structural genes of Erwinia chrysanthemi (EC16) and characterization of the enzymes produced in Escherichia coli
Mol. Gen. Genet.
209
319-325
1987
Dickeya chrysanthemi, Dickeya chrysanthemi EC16
Pissavin, C.; Robert-Baudouy, J.; Hugouvieux-Cotte-Pattat, N.
Biochemical characterization of the pectate lyase PelZ of Erwinia chrysanthemi 3937
Biochim. Biophys. Acta
1383
188-196
1998
Dickeya chrysanthemi, Dickeya chrysanthemi 3937
Roy, C.; Kester, H.; Visser, J.; Shevchik, V.; Hugouvieux-Cotte-Pattat, N.; Robert-Baudouy, J.; Benen, J.
Modes of action of five different endopectate lyases from Erwinia chrysanthemi 3937 [published erratum appears in J Bacteriol 1999 Sep;181(18):5889
J. Bacteriol.
181
3705-3709
1999
Dickeya chrysanthemi, Dickeya chrysanthemi 3937
Tardy, F.; Nasser, W.; Robert-Baudouy, J.; Hugouvieux-Cotte-Pattat, N.
Comparative analysis of the five major Erwinia chrysanthemi pectate lyases: enzyme characteristics and potential inhibitors
J. Bacteriol.
179
2503-2511
1997
Dickeya chrysanthemi
Doan, C.N.; Caughron, M.K.; Myers, J.C.; Breakfield, N.W.; Oliver, R.L.; Yoder, M.D.
Purification, crystallization and X-ray analysis of crystals of pectate lyase A from Erwinia chrysanthemi
Acta Crystallogr. Sect. D
56
351-353
2000
Dickeya chrysanthemi, Dickeya chrysanthemi EC16
-
Thomas, L.M.; Doan, C.N.; Oliver, R.L.; Yoder, M.D.
Structure of pectate lyase A: comparison to other isoforms
Acta Crystallogr. Sect. D
58
1008-1015
2002
Dickeya chrysanthemi, Dickeya chrysanthemi EC16
Dehdashti, S.J.; Doan, C.N.; Chao, K.L.; Yoder, M.D.
Effect of mutations in the T1.5 loop of pectate lyase A from Erwinia chrysanthemi EC16
Acta Crystallogr. Sect. D
59
1339-1342
2003
Dickeya chrysanthemi, Dickeya chrysanthemi EC16
Hurlbert, J.C.; Preston, J.F.3rd.
Functional implications of the b-helical protein fold: Differences in chemical and thermal stabilities of Erwinia chrysanthemi EC16 pectate lyases B, C, and E
Arch. Biochem. Biophys.
381
264-272
2000
Dickeya chrysanthemi, Dickeya chrysanthemi EC16
Kamen, D.E.; Griko, Y.; Woody, R.W.
The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein
Biochemistry
39
15932-15943
2000
Dickeya chrysanthemi
Herron, S.R.; Scavetta, R.D.; Garrett, M.; Legner, M.; Jurnak, F.
Characterization and implications of Ca2+ binding to pectate lyase C
J. Biol. Chem.
278
12271-12277
2003
Dickeya chrysanthemi
Jenkins, J.; Shevchik, V.E.; Hugouvieux-Cotte-Pattat, N.; Pickersgill, R.W.
The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi
J. Biol. Chem.
279
9139-9145
2004
Dickeya chrysanthemi
Scavetta, R.D.; Herron, S.R.; Hotchkiss, A.T.; Kita, N.; Keen, N.T.; Benen, J.A.E.; Kester, H.C.M.; Visser, J.; Jurnak, F.
Structure of a plant cell wall fragment complexed to pectate lyase C
Plant Cell
11
1081-1092
1999
Dickeya chrysanthemi
Herron, S.R.; Benen, J.A.E.; Scavetta, R.D.; Visser, J.; Jurnak, F.
Structure and function of pectic enzymes: virulence factors of plant pathogens
Proc. Natl. Acad. Sci. USA
97
8762-8769
2000
Dickeya chrysanthemi
Castang, S.; Shevchik, V.E.; Hugovieux-Cotte-Pattat, N.; et.al.
Crystallization of the pectate lyase PelI from Erwinia chrysanthemi and SAD phasing of a golf derivative
Acta Crystallogr. Sect. D
60
190-192
2004
Dickeya chrysanthemi
Creze, C.; Castang, S.; Derivery, E.; Haser, R.; Hugouvieux-Cotte-Pattat, N.; Shevchik, V.E.; Gouet, P.
The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate
J. Biol. Chem.
283
18260-18268
2008
Dickeya chrysanthemi (O50325), Dickeya chrysanthemi
Yadav, P.K.; Singh, V.K.; Yadav, S.; Yadav, K.D.; Yadav, D.
In silico analysis of pectin lyase and pectinase sequences
Biochemistry
74
1049-1055
2009
Aspergillus oryzae, Aspergillus clavatus (A1C4B8), Aspergillus fischeri (A1D5E3), Penicillium citrinum (A2I7W3), Aspergillus niger (A2QV36), Bacillus subtilis (A4GRK6), Pectobacterium carotovorum (Q04086), Aspergillus fumigatus (Q4WIT0), Dickeya chrysanthemi (Q59419), Aspergillus nidulans (Q5ATC7)
Payasi, A.; Sanwal, R.; Sanwal, G.
Microbial pectate lyases: Characterization and enzymological properties
World J. Microbiol. Biotechnol.
25
1-14
2009
Alkalihalobacillus alcalophilus, Bacillus licheniformis, Bacillus pumilus, Bacillus pumilus BK2, Bacillus sp. (in: Bacteria), Bacillus sp. (in: Bacteria) KSM-P15, Bacillus sp. (in: Bacteria) P4-N, Bacillus sp. (in: Bacteria) TS 47, Bacillus subtilis, Bacillus subtilis 168, Bacillus subtilis SO113, Cellvibrio japonicus, Clostridium cellulovorans, Dickeya chrysanthemi, Dickeya chrysanthemi (P04959), Dickeya chrysanthemi (P0C1A2), Dickeya chrysanthemi (P11073), Dickeya chrysanthemi (P18209), Fusarium solani, Fusarium verticillioides, Niveispirillum irakense, Pseudomonas fluorescens, Pseudomonas marginalis, Pseudomonas viridiflava, Pseudonocardia sp., Thermobifida fusca
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