Information on EC 4.2.2.12 - xanthan lyase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY
4.2.2.12
-
RECOMMENDED NAME
GeneOntology No.
xanthan lyase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
Eliminative cleavage of the terminal beta-D-mannosyl-(1->4)-beta-D-glucuronosyl linkage of the side-chain of the polysaccharide xanthan, leaving a 4-deoxy-alpha-L-threo-hex-4-enuronosyl group at the terminus of the side-chain
show the reaction diagram
-
-
-
-
Eliminative cleavage of the terminal beta-D-mannosyl-(1->4)-beta-D-glucuronosyl linkage of the side-chain of the polysaccharide xanthan, leaving a 4-deoxy-alpha-L-threo-hex-4-enuronosyl group at the terminus of the side-chain
show the reaction diagram
mechanism
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
beta-elimination
-
-
elimination of an alcohol from a polysaccharide
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
xanthan lyase
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
lyase, xanthan
-
-
-
-
xanthan lyase
-
-
CAS REGISTRY NUMBER
COMMENTARY
113573-69-6
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
strain GL1
-
-
Manually annotated by BRENDA team
strain GL1, enzyme is induced by xanthan
-
-
Manually annotated by BRENDA team
strain XL-1, enzyme is induced by xanthan
-
-
Manually annotated by BRENDA team
Paenibacillus alginolyticus XL-1
strain XL-1, enzyme is induced by xanthan
-
-
Manually annotated by BRENDA team
heat-stable, salt-tolerant mixed culture NRRL B-14401
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
pyruvylated xanthan
pyruvylate mannose + oligosaccharides
show the reaction diagram
-
best substrate
-
?
xanthan
oligosaccharides
show the reaction diagram
-
-
-
?
xanthan
oligosaccharides
show the reaction diagram
-
-
-
?
xanthan
oligosaccharides
show the reaction diagram
-
enzyme is active on polysaccharides with and without acetate and pyruvate, the optimal size of the substrate appears to be in the range of degree of polymerization (DP) 25-35, i.e. 5-7 repeat units of the polysaccharide, no activity against xanthan modified by reduction of the carbonyl groups or by addition of amine or hydroxylethyl groups
the combined action of lyase and endoglucanase yields a series of oligosaccharides, each with a side-chain terminating in an unsaturated uronic acid and containing the molar ratio of D-glucose to D-mannose 2:1
?
xanthan
oligosaccharides
show the reaction diagram
Paenibacillus alginolyticus XL-1
-
-
-
?
xanthan
oligosaccharide
show the reaction diagram
-
-
-
?
xanthan
pyruvylate mannose + oligosaccharide
show the reaction diagram
-
-
-
-
?
xanthan
D-xylooligosaccharides
show the reaction diagram
-
-
-
-
?
additional information
?
-
-
no substrate: p-nitrophenyl-beta-D-mannose, unsubstituted terminal beta-D-mannose residues of xanthan
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
xanthan
oligosaccharide
show the reaction diagram
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Co2+
-
1 mM, slight stimulation
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
4,6-O-[(1S)-1-carboxyethylidene]-beta-D-mannopyranose
-
-
CuCl2
-
0.1 mM, 70% loss of activity
EDTA
-
1 mM, 30% loss of activity
HgCl2
-
1 mM, 95% loss of activity
HgCl2
-
0.1 mM, complete inhibition
NaCl
-
150 mM, 70% loss of activity
NaCl
-
below 10 mM, not, at 85 mM, 60% loss of activity
iodoacetamide
-
1 mM, 70% loss of activity
additional information
-
not inhibitory: CoCl2, MgCl2, CaCl2 at 1 mM
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
2-mercaptoethanol
-
1 mM, slight stimulation
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
additional information
-
Xanthan
-
0.25 mg/ml, wild-type
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
9.92
-
Xanthan
-
30C, pH 5.5, mutant enzyme R313A
1730
-
Xanthan
-
30C, pH 5.5, Y315F
2170
-
Xanthan
-
wild-type
2170
-
Xanthan
-
30C, pH 5.5, wild-type enzyme
6120
-
Xanthan
-
30C, pH 5.5, R612A
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
2.21
-
4,6-O-[(1S)-1-carboxyethylidene]-beta-D-mannopyranose
-
30C, pH 5.5, wild type enzyme
19.2
-
4,6-O-[(1S)-1-carboxyethylidene]-beta-D-mannopyranose
-
30C, pH 5.5,mutant enzyme R612A
4
10
D-mannose
-
30C, pH 5.5,mutant enzyme R612A
837
-
D-mannose
-
30C, pH 5.5, wild type enzyme
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
2.62
-
-
30C, pH 6.9
6.28
-
-
pH 7.0
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5
-
-
plus 0.05 M NaCl
5.5
-
-
-
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6.5
9
-
at 4C
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
50
-
-
-
pI VALUE
pI VALUE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
3.7
-
-
isoelectric focusing
7.9
-
-
isoelectric focusing
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
excreted to medium
-
Manually annotated by BRENDA team
-
excreted to medium
-
Manually annotated by BRENDA team
-
excreted to medium
-
Manually annotated by BRENDA team
Paenibacillus alginolyticus XL-1
-
excreted to medium
-
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Bacillus sp. (strain GL1)
Bacillus sp. (strain GL1)
Bacillus sp. (strain GL1)
Bacillus sp. (strain GL1)
Bacillus sp. (strain GL1)
Bacillus sp. (strain GL1)
Bacillus sp. (strain GL1)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
33000
-
-
gel filtration
75000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 85000, SDS-PAGE
?
-
x * 100000, SDS-PAGE, deduced from gene sequence: enzyme has a 36 amino acid signal sequence, mature enzyme has 97000 Da
?
Paenibacillus alginolyticus XL-1
-
x * 100000, SDS-PAGE, deduced from gene sequence: enzyme has a 36 amino acid signal sequence, mature enzyme has 97000 Da; x * 85000, SDS-PAGE
-
monomer
-
1 * 75000, SDS-PAGE
monomer
-
1 * 33000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
hanging-drop vapour-diffusion, resolution of N194A/PyrMan, N194/pentasacharide and ligand-free form are 1.8, 2.1 and 2.3 respectively
-
structure of wild-type enzyme, wild type enzyme in complex with ryruvated D-mannose and mutant enzyme R612A, hanging-drop vapor diffusion
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TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
45
-
-
pH 7.0, 10 min, loss of 60% of activity
45
-
-
not stable above
55
-
-
20 mM sodium phosphate, pH 5.0, 0.25 M NaCl, stable for 6h
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
partial
-
expression of wild-type and mutant enzymes in Escherichia coli
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
H246A
-
mutant with 2fold decreased Km for xanthan, 500fold decreased turnover number
N194A
-
mutant with 2fold decreased Km for xanthan, 570fold decreased turnover number
Y255F
-
mutant with 2fold decreased Km for xanthan, 360fold decreased turnover number
R313A
-
KM-value for xanthan is 1.5fold higher than wild type value. kcat for xanthan is 219fold lower than wild-type value
R612A
-
KM-value for xanthan is 11.6fold higher than wild type value. kcat for xanthan is 2.8fold higher than wild-type value
Y315F
-
KM-value for xanthan is 1.8fold higher than wild type value. kcat for xanthan is 1.3fold lower than wild-type value