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Information on EC 4.2.2.10 - pectin lyase and Organism(s) Aspergillus niger and UniProt Accession Q01172
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4.2.2.10 pectin lyaseIUBMB Comments
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.
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Word Map
- 4.2.2.10
- cellulase
- xylanase
- aspergillus
- polysaccharide
- polygalacturonase
- juice
- niger
-
pectinolytic
- amylase
- pulp
- peel
- pectate
- penicillium
- citrus
- erwinia
-
saccharification
-
hemicellulase
- polygalacturonic
-
methylesterase
- lyases
- xylan
- bran
- endo-polygalacturonase
- rhamnogalacturonan
-
wall-degrading
- glucanase
-
enzyme-assisted
-
cellulolytic
- carotovora
- pectinesterase
- cellobiase
- tannase
- homogalacturonans
- chrysanthemi
- cmcase
-
box-behnken
-
3.2.1.15
- nutrition
- synthesis
- fibrobacter
- pomace
-
scouring
- industry
- mannanase
- oligogalacturonides
- bagasse
- flavefaciens
- agriculture
-
d-galacturonic
-
degumming
- food industry
-
carbohydrases
-
agro-industrial
- ruminicola
-
cazymes
The taxonomic range for the selected organisms is: Aspergillus niger
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
Synonyms
pectinase, pectin lyase, pectin lyase a, pectinlyase, commercial pectic enzyme, pnl-zj5a, endo-pectin lyase, pectolyase y23, pectin methyltranseliminase, poly(methoxygalacturonide) lyase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
endo-pectin lyase
-
-
-
-
lyase, pectin
-
-
-
-
pectin methyltranseliminase
-
-
-
-
pectin transeliminase
-
-
-
-
PL
Pla
PLB
-
-
-
-
PLD
-
-
-
-
PLI
-
-
-
-
PLII
-
-
-
-
PNL
poly(methoxygalacturonide) lyase
-
-
-
-
polymethylgalacturonic transeliminase
-
-
-
-
Ultrazym-100
PL
-
-
-
-
Pla
-
-
-
-
PNL
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
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
reaction mechanism, catalytic residues Arg236, Arg176, and Lys239 are essentially involved in catalysis
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
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
reaction mechanism
-
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
favours pectin, the methylester, 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
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
elimination
elimination
-
-
-
-
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
9033-35-6
-
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
partially methyl-esterified pectin
?
prepared from citrus and Aspergillus sp.
-
-
?
pectin with 70% methyl esterification
?
-
44% of the activity with citrus pectin
-
-
?
pectin with 85% methyl esterification
?
-
118% of the activity with citrus pectin
-
-
?
additional information
?
-
pH driven conformational changes of the enzyme, wild-type and mutants
-
-
?
additional information
?
-
-
pH driven conformational changes of the enzyme, wild-type and mutants
-
-
?
additional information
?
-
-
substrate specificity, activity increases with increasing length of the substrate up to polymerization degree of 8 monomers, enzyme is very specific for fully methyl-esterified oligogalacturonides, removal of the methyl-ester or changing the type of ester, e.g. ethyl esterification, or transamidation result in almost complete loss of activity, enzyme is capable of cleaving the bond between a methyl-esterified and a non-esterified galacturonic acid residue, where the newly formed DELTA4,5 unsaturated non-reducing end residue always contains a methyl-ester, product determination by mass spectrometry
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Na+
Ca2+
-
optimal concentration above pH 4.5: 50 mM. Optimal cocentration below pH 4.5: 30 mM
Na+
-
optimal concentration above pH 4.5: 300 mM. Optimal concentration below pH 4.5: 100 mM
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
kinetics of wild-type and mutant enzymes, influence of pH on the kinetics
-
additional information
additional information
-
kinetics of wild-type and mutant enzymes, influence of pH on the kinetics
-
additional information
additional information
-
subsite affinities, kinetics
-
additional information
additional information
-
Km-value of 2.2 mg/ml for pectin
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
32
-
purified enzyme, McIlvaine buffer with 0.1 M citrate and 0.2 M phosphate
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
LITERATURE
TEMPERATURE OPTIMUM
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
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
-
pectin lyase acts on the pectic substances that occur as structural polysaccharides in the middle lamella and primary cell walls of higher plants
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). PELA_ASPNG
379
0
39855
Swiss-Prot
Secretory Pathway (Reliability: 1)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D154A
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
D154E
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
D186N
site-directed mutagenesis, reduced activity and altered pH profile compared to the wild-type enzyme
D186N/D221N
site-directed mutagenesis, reduced activity and altered pH profile compared to the wild-type enzyme
D221N
site-directed mutagenesis, reduced activity and altered pH profile compared to the wild-type enzyme
K239N
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
N109A
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
R176A
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
R176D
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
R176K
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
R236A
site-directed mutagenesis, active site residue exchange, completely inactive mutant
R236K
site-directed mutagenesis, active site residue exchange, completely inactive mutant
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
3.9
-
minimum deactivation rate constant at pH 3.9 and 29°C, deactivation process is modelled as first-order kinetics
654468
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
29
-
minimum deactivation rate constant at pH 3.9 and 29°C, deactivation process is modelled as first-order kinetics
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
high ionic strength or high salt concentration appear to be essential for enzyme stability
-
impact of glass transition on inactivation kinetics, glass transition temperature is decreased by ultrafiltration
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
24°C, in the glassy state, enzyme is completely stable for 7 days, after that the activity is lost, inactivation kinetics, different temperatures and moisture levels
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native wild-type enzyme and recombinant mutant enzymes to homogeneity
purification by ammonium sulfate fractionation, gel filtration and ion-exchange chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of mutant enzymes in Aspergillus niger strain NW188, subcloning in Escherichia coli DH5alpha
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
food industry
synthesis
food industry
-
application for clarification of fruit juice. For apple, orange, pomegranate juices treated with the partially purified enzyme, the clarity values are 219.74, 206.38 and 203.48%, respectively
food industry
-
pectin lyase PNL-ZJ5A can effectively decrease the viscosity and improve the yield of apple juice and light transmittance
synthesis
-
cheap and simple method of immobilization is attractive for the preparation of tailored systems for industrial application as well as for studies on substrate-enzyme-support interactions
synthesis
-
production of Aspergillus niger on wheat bran and citrus pectin in submerged culture
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Van Houdenhoven, F.E.A.
Studies on pectin lyase
Mededelingen Landbouwhogeschool, Communications Agricultural University
75-13
1-100
1975
Aspergillus niger
-
Mayans, O.; Scott., M.; Connerton, I.; Gravesen, T.; Benen, J.; Visser, J.; Pickersgill, R.; Jenkins, J.
Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases
Structure
5
677-689
1997
Aspergillus niger
Kester, H.C.M.; Visser, J.
Purification and characterization of pectin lyase B, a novel pectinolytic enzyme from Aspergillus niger
FEMS Microbiol. Lett.
120
63-68
1994
Aspergillus niger
-
Hanisch, W.H.; Rickard, P.A.D.; Nyo, S.
Poly(methoxygalacturonide) lyase immobilized via titanium onto solid supports
Biotechnol. Bioeng.
20
95-106
1978
Aspergillus niger
-
Naidu, G.S.N.; Panda, T.
Studies on pH and thermal deactivation of pectolytic enzymes from Aspergillus niger
Biochem. Eng. J.
16
57-67
2003
Aspergillus niger
-
Sanchez-Torres, P.; Visser, J.; Benen, J.A.
Identification of amino acid residues critical for catalysis and stability in Aspergillus niger family 1 pectin lyase A
Biochem. J.
370
331-337
2003
Aspergillus niger (Q01172), Aspergillus niger
Taragano, V.M.; Pilosof, A.M.R.
Calorimetric studies on dry pectinlyase preparations: impact of glass transition on inactivation kinetics
Biotechnol. Prog.
17
775-777
2001
Aspergillus niger, Aspergillus niger 148
Naidu, G.S.N.; Panda, T.
Performance of pectolytic enzymes during hydrolysis of pectic substances under assay conditions: a statistical approach
Enzyme Microb. Technol.
25
116-124
1999
Aspergillus niger, Aspergillus niger NCIM 548
-
van Alebeek, G.J.; Christensen, T.M.; Schols, H.A.; Mikkelsen, J.D.; Voragen, A.G.
Mode of action of pectin lyase A of Aspergillus niger on differently C(6)-substituted oligogalacturonides
J. Biol. Chem.
277
25929-25936
2002
Aspergillus niger, Aspergillus niger 4M-147
Mantovani, C.F.; Geimba, M.P.; Brandelli, A.
Enzymatic clarification of fruit juices by fungal pectin lyase
Food Biotechnol.
19
173-181
2005
Aspergillus niger, Penicillium expansum, Penicillium expansum F16, Penicillium sp., Penicillium sp. CF2
-
Yadav, S.; Shastri, N.V.
Partial purification of an extracellular pectin lyase from a strain of Aspergillus niger
Indian J. Microbiol.
44
201-204
2004
Aspergillus niger
-
Ortega, N.; De Diego, S.; Rodriguez-Nogales, J.M.; Perez-Mateos, M.; Busto, M.D.
Kinetic behaviour and thermal inactivation of pectinlyase used in food processing
Int. J. Food Sci. Technol.
39
631-639
2004
Aspergillus niger
-
Yadav, S.; Yadav, P.; Yadav, D.; Yadav, K.
Pectin lyase: A review
Process Biochem.
44
1-10
2009
Aspergillus ficuum, Aspergillus flavus, Aspergillus japonicus, Aspergillus niger, Aspergillus oryzae, Aspergillus sojae, Paenibacillus amylolyticus, Bacillus sp. (in: Bacteria), Colletotrichum lindemuthianum, Fusarium oxysporum, Penicillium expansum, Penicillium italicum, Penicillium paxilli, Penicillium viridicatum, Pseudomonas fluorescens, Pseudomonas marginalis, Rhizoctonia solani, Rhizopus arrhizus, Cystofilobasidium capitatum, Penicillium canescens, Alternaria mali, Globisporangium splendens, Pectobacterium aroidearum, Bacillus sp. (in: Bacteria) PN 33
-
Poturcu, K.; Ozmen, I.; Biyik, H.
Characterization of an alkaline thermostable pectin lyase from newly isolated Aspergillus niger _WHAK1 and its application on fruit juice clarification
Arab. J. Sci. Eng.
42
19-29
2017
Aspergillus niger, Aspergillus niger WHAK1
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