Information on EC 3.2.1.81 - beta-agarase

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The expected taxonomic range for this enzyme is: Bacteria, Archaea

EC NUMBER
COMMENTARY hide
3.2.1.81
-
RECOMMENDED NAME
GeneOntology No.
beta-agarase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Hydrolysis of (1->4)-beta-D-galactosidic linkages in agarose, giving the tetramer as the predominant product
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of O-glycosyl bond
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
agarose degradation
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porphyran degradation
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SYSTEMATIC NAME
IUBMB Comments
agarose 4-glycanohydrolase
Also acts on porphyran, but more slowly [1]. This enzyme cleaves the beta-(1->4) linkages of agarose in a random manner with retention of the anomeric-bond configuration, producing beta-anomers that give rise progressively to alpha-anomers when mutarotation takes place [6]. The end products of hydrolysis are neoagarotetraose and neoagarohexaose in the case of AgaA from the marine bacterium Zobellia galactanivorans, and neoagarotetraose and neoagarobiose in the case of AgaB [6].
CAS REGISTRY NUMBER
COMMENTARY hide
37288-57-6
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
; strain AG LSL-1, enzyme is inducible by agar and not repressed by other simple sugars. NaCl is not required for growth or production of agarase. Enzyme belongs to group III beta-agarase family
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Manually annotated by BRENDA team
strain AG LSL-1, enzyme is inducible by agar and not repressed by other simple sugars. NaCl is not required for growth or production of agarase. Enzyme belongs to group III beta-agarase family
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
Agarivorans sp.
strain JAMB-A11
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
strain C-1
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Manually annotated by BRENDA team
animal
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
Cellvibrio sp.
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
Microbulbifer sp.
Microbulbifer sp. CMC-5 (MTCC 9889)
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Manually annotated by BRENDA team
Microbulbifer sp. JAMB-A94
strain JAMB-A94
UniProt
Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
strain N-1
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
strain SK38
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Manually annotated by BRENDA team
Pseudomonas-like bacterium
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
strain F-6
Uniprot
Manually annotated by BRENDA team
strain JT0107
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Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
strain V134
UniProt
Manually annotated by BRENDA team
strain V143
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
Dsij
UniProt
Manually annotated by BRENDA team
strain KCTC 12921
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Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
agar + H2O
?
show the reaction diagram
agar + H2O
neoagarobiose + neoagarotetraose + neoagarohexaose
show the reaction diagram
agar + H2O
neoagarohexaose + neoagarotetraose
show the reaction diagram
-
-
-
-
?
agar + H2O
neoagarooctaose + neoagarohexaose + neoagarotetraose
show the reaction diagram
-
-
-
?
agar + H2O
neoagarotetraose + neoagarohexaose
show the reaction diagram
agaropectin + H2O
?
show the reaction diagram
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-
-
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ir
agarose + H2O
2 neoagarooligosaccharides
show the reaction diagram
rAgaC with low activity (0.05 U/ml) cleaves agarose into longer neoagarooligosaccharides. When activity is increased to 30 U/ml, neoagarooctaose is produced predominantly in addition to neoagarohexaose and neoagarotetraose
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-
?
agarose + H2O
?
show the reaction diagram
agarose + H2O
agarotetraose
show the reaction diagram
agarose + H2O
neoagarobiose
show the reaction diagram
agarose + H2O
neoagarobiose + neoagarotetraose
show the reaction diagram
agarose + H2O
neoagarobiose + neoagarotetraose + neoagarohexaose
show the reaction diagram
agarose + H2O
neoagarohexaose + neoagarotetraose
show the reaction diagram
agarose + H2O
neoagarohexaose + neoagarotetraose + neoagarobiose
show the reaction diagram
agarose + H2O
neoagarooctaose + ?
show the reaction diagram
agarose + H2O
neoagarooctaose + neoagarodecaose
show the reaction diagram
agarose + H2O
neoagarosebiose
show the reaction diagram
agarose + H2O
neoagarotetraose
show the reaction diagram
agarose + H2O
neoagarotetraose + ?
show the reaction diagram
agarose + H2O
neoagarotetraose + neoagarobiose
show the reaction diagram
agarose + H2O
neoagarotetraose + neoagarohexaose
show the reaction diagram
agarose + H2O
neoagarotetraose + neoagarohexaose + neoagarobiose
show the reaction diagram
agarose + H2O
neoagarotetraose + neoagarohexaose + neoagarooctaose
show the reaction diagram
alginate + H2O
?
show the reaction diagram
Microbulbifer sp.
-
-
-
-
?
alkali treated porphyran + H2O
?
show the reaction diagram
carboxymethyl cellulose + H2O
?
show the reaction diagram
carrageenan + H2O
?
show the reaction diagram
Microbulbifer sp.
-
-
-
-
?
chitin + H2O
?
show the reaction diagram
neoagaro-oligosaccharides + H2O
?
show the reaction diagram
-
from N2 to N22, reaction yield for neoagaro-oligosaccharides is 52.7% by 4 U/mg beta-agarase
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?
neoagarodecaose + H2O
?
show the reaction diagram
is a very poor substrate
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?
neoagarododecaose + H2O
?
show the reaction diagram
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?
neoagarododecaose + H2O
neoagarohexaose + neoagarotetraose + neoagarooctaose
show the reaction diagram
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?
neoagarohexaitol + H2O
?
show the reaction diagram
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ir
neoagarohexaose + H2O
?
show the reaction diagram
neoagarohexaose + H2O
neoagarobiose
show the reaction diagram
neoagarohexaose + H2O
neoagarobiose + neoagarotetraose
show the reaction diagram
neoagarohexaose + H2O
neoagarotetraose + neoagarobiose
show the reaction diagram
neoagarooctaose + H2O
neoagarobiose + neoagarotetraose + neoagarohexaose
show the reaction diagram
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-
?
neoagarooctaose + H2O
neoagarohexaose + neoagarobiose
show the reaction diagram
neoagarooctaose + H2O
neoagarohexaose + neoagarotetraose + neoagarobiose
show the reaction diagram
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-
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?
neoagarooctaose + H2O
neoagarotetraose
show the reaction diagram
neoagarotetradecaose + H2O
?
show the reaction diagram
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?
neoagarotetraose + H2O
neoagarobiose
show the reaction diagram
polysaccharides with neoagarobiose units + H2O
neoagarobiose + neoagarotetraose
show the reaction diagram
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ir
porphyran + H2O
neoagaro-oligosaccharides
show the reaction diagram
porphyran + H2O
neoagarohexaose + neoagarotetraose
show the reaction diagram
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?
porphyran + H2O
neoagarooctaose + neoagarohexaose + neoagarotetraose
show the reaction diagram
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?
xylan + H2O
?
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
agar + H2O
neoagarobiose + neoagarotetraose + neoagarohexaose
show the reaction diagram
agar + H2O
neoagarotetraose + neoagarohexaose
show the reaction diagram
agarose + H2O
neoagarobiose
show the reaction diagram
agarose + H2O
neoagarobiose + neoagarotetraose + neoagarohexaose
show the reaction diagram
agarose + H2O
neoagarohexaose + neoagarotetraose + neoagarobiose
show the reaction diagram
agarose + H2O
neoagarooctaose + ?
show the reaction diagram
agarose + H2O
neoagarooctaose + neoagarodecaose
show the reaction diagram
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major products
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?
agarose + H2O
neoagarotetraose
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
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135% activity at 1 mM
Cu2+
1 mM, increases activity of agarase AG-b 1.2fold
Fe2+
2 mM stimulates agarase activity by 20%
KCl
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no activity in the presence of 00.3 M salt. The enzyme shows a salt requirement for activity, being active from 0.3 M NaCl, with maximal activity at 3.5 M NaCl. KCl supports similar activities as NaCl up to 3.5 M, and LiCl up to 2.5 M. The monovalent salts can not be substituted by 3.5 M divalent cations, CaCl2 or MgCl2
LiCl
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no activity in the presence of 00.3 M salt. The enzyme shows a salt requirement for activity, being active from 0.3 M NaCl, with maximal activity at 3.5 M NaCl. KCl supports similar activities as NaCl up to 3.5 M, and LiCl up to 2.5 M. The monovalent salts can not be substituted by 3.5 M divalent cations, CaCl2 or MgCl2
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-ethyl-(3-(3-dimethyl-amino-)propyl)carbonate
Microbulbifer sp.
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1 mM. 10-20% inhibition
5,5'-dithiobis-(2-nitrobenzoic acid)
53% residual activity at 10 mM
Ag+
5 mM, complete inhibition of agarase AG-b
AgNO3
AlCl3
Ba2+
Microbulbifer sp.
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85% residual activity at 1 mM
Co2+
Microbulbifer sp.
-
complete inhibition at 1 mM
CuCl2
CuSO4
diethyl dicarbonate
Microbulbifer sp.
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1 mM, 10-20% inhibition
EGTA
-
the inhibition by 1 mM EGTA is almost completely recovered by the addition of Co2+ at a concentration of 0.2 mM
FeCl2
-
2 mM, 99% inhibition
FeCl3
-
partially inhibits the activity
HgCl2
K+
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94.9% residual activity at 100 mM
KCl
-
50% inhibition at 0.1 M
L-galactose 6-sulfate
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MnCl2
-
partially inhibits the activity
N-bromosuccinimide
NH4Cl
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50% inhibition at 0.1 M
Pb(CH3COO)2
PbCl2
-
2 mM, 98% inhibition
sodium dodecylsulfate
ZnCl2
ZnSO4
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanol
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30% increase in activity
beta-mercaptoethanol
beta-mercaptoethanol even at a low concentration of 10 mM increases the activity of AgaA by 23%
CaCl2
-
stimulation
dithiothreitol
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0182 - 4.2
agarose
1 - 2
liquid-phase agarose
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12.81
neoagarodecaose
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12.39
neoagarododecaose
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1.7
neoagarohexaose
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8.36
neoagarotetradecaose
-
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
22 - 41
agarose
0.19
neoagarodecaose
Pseudoalteromonas sp. CY24
A1A3Y9
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4.77
neoagarododecaose
Pseudoalteromonas sp. CY24
A1A3Y9
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5.16
neoagarotetradecaose
Pseudoalteromonas sp. CY24
A1A3Y9
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5.3
agarose
Saccharophagus degradans
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in 20 mM Tris-HCl buffer (pH 7.0), at 30C
2642
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1
KCl
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.04
Microbulbifer sp.
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culture supernatant, pH 7.0, 30C
0.1
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AgaB, 1 ml of 0.125% melted agarose, 44C, pH 7.5
0.16
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AgaAc, 1 ml of 0.125% melted agarose, 44C, pH 7.5
0.7
Cellvibrio sp.
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crude enzyme from culture fluid, in 50 mM phosphate buffer, pH 7.0, 35C
0.872
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cell lysate
0.9
Agarivorans sp.
cell-free extract, at pH 7.0 and 35C
1.2
-
wild-type
3
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cell-free medium, at pH 7.0 and 35C
4.13
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concentrated agarase solution
4.22
Microbulbifer sp.
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after 103.5fold purification, pH 7.0, 30C
14.2
-
pH 7.0, 40C
16.9
culture fluid
25.5
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40C, pH 8.0
36
mutant enzyme V109G/V110C/T111H/S112L, in 20 mM phosphate buffer (pH 6.5) containing 0.25% (w/v) agarose at 40C for 10 min
57.45
-
agarase Hz-c, 13.9fold purified
63.6
-
catalytic module
76.8
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agarase Hz-b, 18.6fold purified
83.5
-
35C, pH 7.0; after 27.8fold purification, at pH 7.0 and 35C
84.2
Cellvibrio sp.
-
after 120.2fold purification, in 50 mM phosphate buffer, pH 7.0, 35C
167
Agarivorans sp.
-
pH 8.0, 40C
204.4
using agar as substrate, in pH 5.5 acetate buffer, at 45C
207.5
using agarose as substrate, in pH 5.5 acetate buffer, at 45C
208.1
Agarivorans sp.
purified enzyme, at pH 7.0 and 35C
230.1
agarase AG-a
242.2
15fold purified rAgaB34, with agarose as substrate at 40C
329
-
recombinant AgaC
371
Agarivorans sp.
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50 mM N-tris(hydroxymethyl)methyl-3-aminopropanesulfonic acid-NaOH buffer, pH 7.8, containing 10 mM CaCl2, 0.1 mM NaCl, 40C
466
mutant enzyme N103T, in 20 mM phosphate buffer (pH 6.5) containing 0.25% (w/v) agarose at 40C for 10 min
475
mutant enzyme S182I, in 20 mM phosphate buffer (pH 6.5) containing 0.25% (w/v) agarose at 40C for 10 min
482
wild type enzyme, in 20 mM phosphate buffer (pH 6.5) containing 0.25% (w/v) agarose at 40C for 10 min
1600
-
purified refolded AgaB
5000
recombinant AgaB 476fold purified
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.2
-
porphyran as substrate
6 - 9
Agarivorans sp.
-
6.5 - 7.5
native enzyme
6.7
Pseudomonas-like bacterium
-
beta-agarase I and IIb
6.8
-
porphyran as substrate
7.4
-
porphyran as substrate
7.5 - 8
Agarivorans sp.
-
Britton-Robinson universal buffers, MOPS and N-tris(hydroxymethyl)methyl-3-aminopropanesulfonic acid-NaOH buffer
additional information
-
mutant L122Q/N446I has comparable optimum pH as the wild-type
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 9
-
the enzyme shows more than 90% activity between pH 5.0 and 8.0. More than 50% of the agarase activity is lost below pH 4.0 and above pH 9.0
4 - 8
-
-
4.5 - 7.5
the enzyme retains its activity up to 60% at pH 4.5-7.5
5 - 8
-
pH 5.0: about 35% of maximal activity, about 40% of maximal activity
5 - 8.5
5 - 9
-
about 60% of activity
5 - 10
pH 5.0: about 65% of maximal activity, pH 10.0: about 75% of maximal activity, agarase AG-a
5.5 - 7.5
Cellvibrio sp.
-
the agarase exhibits more than 90% of the maximum activity in the pH range of 5.5 to 7.5
5.5 - 8
-
-
6 - 9
-
more than 80% of maximum activity
6 - 8
Agarivorans sp.
the enzyme activity is about 80% at pH 6.0 and less than 60% over pH 8.0
6 - 8
Cellvibrio sp.
more than 50% activity between pH 6.0 and 8.0. The activity gradually decreases at alkaline pH and significantly declines at acidic pH
6 - 8
Microbulbifer sp.
-
the agarase retains more than 70% of its original activity at pH 6.0 and 8.0
6 - 9
-
more than 80% of the maximal activity retained
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20 - 40
34
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porphyran as substrate
38
Pseudomonas-like bacterium
-
beta-agarase I
38 - 55
native enzyme
40 - 41
-
-
42.5
Cellvibrio sp.
-
43
Pseudomonas-like bacterium
-
beta-agarase IIb
54
Microbulbifer sp.
-
-
60
Agarivorans sp.
-
more than 70% of maximum activity
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20
-
30% of maximum activity
25 - 55
Agarivorans sp.
the enzyme activity is more than 80% at 25C and 45C and less than 10% over 55C
25 - 47
Cellvibrio sp.
more than 50% activity between 25 and 47C. The enzyme activity drastically decreases over 45C
25 - 40
-
the enzyme works efficiently in the range of 25-40C and shows maximum activity at 40C but loses essentially all of its activity at 60C
25 - 70
25C: about 60% of maximal activity, 70C: about 80% of maximal activity, agarase AG-a
30
-
90% of maximum activity
40 - 50
Cellvibrio sp.
-
the agarase exhibits more than 90% of the maximum activity in the temperature ranging from 40C to 50C
45 - 85
-
45C: about 50% of maximal activity, 85C: about 55% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.1
-
calculated
5.4
calculated from amino acid sequence
5.9
calculated from amino acid sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)
Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)
Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)
Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)
Zobellia galactanivorans (strain DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij)
Zobellia galactanivorans (strain DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij)
Zobellia galactanivorans (strain DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij)
Zobellia galactanivorans (strain DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij)
Zobellia galactanivorans (strain DSM 12802 / CIP 106680 / NCIMB 13871 / Dsij)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
13400
-
AgaAc, calculated by sequence
20000
-
SDS-PAGE
21000
-
SDS-PAGE
26500
-
gel filtration
29000
-
calculation from sequence of DNA
31000
recombinant enzyme
32150
-
AgaAc, ESI MS
35130
-
calculation from sequence of an open reading frame
37000
recombinant enzyme
40010
-
AgaB, ESI MS
47240
-
sequence analysis
48200
Microbulbifer sp.
-
calculated from sequence
48400
calculated from amino acid sequence
50900
sequence analysis
51200
calculated from amino acid sequence
56000
-
gel filtration
58000
Agarivorans sp.
-
60000
recombinant enzyme
61000
Pseudomonas-like bacterium
-
gel filtration, beta-agarase IIb
63000
-
SDS-PAGE
63600
Pseudomonas-like bacterium
-
analytical ultracentrifugation, beta-agarase IIb
65020
Microbulbifer sp.
-
calculated from sequence
72000
-
SDS-PAGE
72500
maltose binding protein-fused enzyme, SDS-PAGE
79000
Cellvibrio sp.
gel filtration
82000
-
SDS-PAGE
84000
-
His-tagged recombinant enzyme, SDS-PAGE
87500
native enzyme
100000
105000
106100
-
sequence analysis
109000
Agarivorans sp.
recombinant enzyme
113000
127000
Pseudomonas-like bacterium
-
gel filtration, beta-agarase I
140000
Pseudomonas-like bacterium
-
SDS-PAGE, beta-agarase I
180000
-
gel filtration
210000
Pseudomonas-like bacterium
-
analytical ultracentrifugation, beta-agarase I
353000
-
AgaB, calculated by sequence
539000
-
AgaA, calculated by sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
monomer
additional information