BRENDA - Enzyme Database show
show all sequences of 4.2.2.8

Crystal structure of Pedobacter heparinus heparin lyase Hep III with the active site in a deep cleft

Hashimoto, W.; Maruyama, Y.; Nakamichi, Y.; Mikami, B.; Murata, K.; Biochemistry 53, 777-786 (2014)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
isoform Hep III, to 2.2 A resolution. The enzyme comprises an N-terminal alpha/alpha-barrel domain and a C-terminal antiparallel beta-sheet domain as its basic scaffold. Isoform Hep III exhibits an open form compared with the closed form of Hep II. An active site of Hep III is located in the deep cleft at the interface between its two domains
Pedobacter heparinus
Engineering
Amino acid exchange
Commentary
Organism
E237A
40.8% of wild-type activitiy
Pedobacter heparinus
F423A
42.4% of wild-type activitiy
Pedobacter heparinus
H241A
29.7% of wild-type activitiy
Pedobacter heparinus
H424A
0.3% of wild-type activitiy
Pedobacter heparinus
I29V/L657S
42.7% of wild-type activitiy
Pedobacter heparinus
N240A
3.1% of wild-type activitiy
Pedobacter heparinus
Q238A
88.5% of wild-type activitiy
Pedobacter heparinus
W350A
27.7% of wild-type activitiy
Pedobacter heparinus
Y294F
2.8% of wild-type activitiy
Pedobacter heparinus
Y450F
5.6% of wild-type activitiy
Pedobacter heparinus
Y590
7.7% of wild-type activitiy
Pedobacter heparinus
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Pedobacter heparinus
Q59289
-
-
Pedobacter heparinus DSM 2366
Q59289
-
-
Temperature Stability [°C]
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
39.4
-
melting temperature, presence of 1 mM heparin tetrasaccharide
Pedobacter heparinus
40.5
-
melting temperature, presence of 0.1 mM heparin tetrasaccharide
Pedobacter heparinus
43.9
-
melting temperature, presence of 0.1 mM heparin disaccharide
Pedobacter heparinus
44.3
-
melting temperature, presence of 0.1 mM N-acetyl glucosamine
Pedobacter heparinus
45.2
-
melting temperature, presence of 0.1 mM gellan tetrasaccharide
Pedobacter heparinus
45.44
-
melting temperature
Pedobacter heparinus
Crystallization (Commentary) (protein specific)
Crystallization
Organism
isoform Hep III, to 2.2 A resolution. The enzyme comprises an N-terminal alpha/alpha-barrel domain and a C-terminal antiparallel beta-sheet domain as its basic scaffold. Isoform Hep III exhibits an open form compared with the closed form of Hep II. An active site of Hep III is located in the deep cleft at the interface between its two domains
Pedobacter heparinus
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
E237A
40.8% of wild-type activitiy
Pedobacter heparinus
F423A
42.4% of wild-type activitiy
Pedobacter heparinus
H241A
29.7% of wild-type activitiy
Pedobacter heparinus
H424A
0.3% of wild-type activitiy
Pedobacter heparinus
I29V/L657S
42.7% of wild-type activitiy
Pedobacter heparinus
N240A
3.1% of wild-type activitiy
Pedobacter heparinus
Q238A
88.5% of wild-type activitiy
Pedobacter heparinus
W350A
27.7% of wild-type activitiy
Pedobacter heparinus
Y294F
2.8% of wild-type activitiy
Pedobacter heparinus
Y450F
5.6% of wild-type activitiy
Pedobacter heparinus
Y590
7.7% of wild-type activitiy
Pedobacter heparinus
Temperature Stability [°C] (protein specific)
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
39.4
-
melting temperature, presence of 1 mM heparin tetrasaccharide
Pedobacter heparinus
40.5
-
melting temperature, presence of 0.1 mM heparin tetrasaccharide
Pedobacter heparinus
43.9
-
melting temperature, presence of 0.1 mM heparin disaccharide
Pedobacter heparinus
44.3
-
melting temperature, presence of 0.1 mM N-acetyl glucosamine
Pedobacter heparinus
45.2
-
melting temperature, presence of 0.1 mM gellan tetrasaccharide
Pedobacter heparinus
45.44
-
melting temperature
Pedobacter heparinus
Other publictions for EC 4.2.2.8
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
748820
Gu
Photoswitchable heparinase II ...
Pedobacter heparinus
Org. Lett.
20
48-51
2018
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747456
Hu
Probing cleavage promiscuity ...
Pedobacter heparinus
Carbohydr. Polym.
173
276-285
2017
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16
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747570
Gu
Expanding the catalytic promi ...
Pedobacter heparinus
Chemistry
23
2548-2551
2017
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3
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5
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2
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3
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5
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747916
Ulaganathan
Conformational flexibility of ...
Bacteroides thetaiotaomicron, Bacteroides thetaiotaomicron DSM 2079
Glycobiology
27
176-187
2017
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-
1
1
3
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1
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4
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1
3
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11
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747454
Carnachan
Determining the extent of hep ...
Pedobacter heparinus
Carbohydr. Polym.
152
592-597
2016
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1
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729269
Hashimoto
Crystal structure of Pedobacte ...
Pedobacter heparinus, Pedobacter heparinus DSM 2366
Biochemistry
53
777-786
2014
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1
11
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6
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730858
Dong
Structural basis of heparan su ...
Bacteroides thetaiotaomicron, Bacteroides thetaiotaomicron DSM 2079
Protein Cell
3
950-961
2012
-
-
1
1
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3
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714553
Chen
Biochemical analysis and kinet ...
Pedobacter heparinus
Biotechnol. Bioeng.
108
1841-1851
2011
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1
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1
1
11
1
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1
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1
1
1
1
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3
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1
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1
1
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11
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1
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1
1
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1
1
1
1
1
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3
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1
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1
1
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701676
Babu
Fluorescent-tagged heparan sul ...
Pedobacter heparinus
Anal. Biochem.
396
124-132
2010
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1
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701885
Hyun
Cloning, overexpression, and c ...
Bacteroides stercoris, Bacteroides stercoris HJ-15
Appl. Microbiol. Biotechnol.
86
879-890
2010
-
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1
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4
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3
2
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3
1
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5
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1
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1
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1
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5
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1
1
1
1
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1
1
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1
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714027
Raman
Differential effects of hepari ...
Pedobacter heparinus
Biochem. Biophys. Res. Commun.
398
191-193
2010
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3
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1
1
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682098
Rops
Heparan sulfate on activated g ...
Pedobacter heparinus
Nephrol. Dial. Transplant.
22
1070-1077
2007
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2
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665613
Wei
Distinct substrate specificiti ...
Pedobacter heparinus
J. Biol. Chem.
280
15742-15748
2005
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3
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664047
Chai
Relative susceptibilities of t ...
Pedobacter heparinus
Biochemistry
43
8590-8599
2004
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649969
Pojasek
Histidine 295 and histidine 51 ...
Pedobacter heparinus
Biochemistry
39
4012-4019
2000
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1
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13
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1
11
-
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2
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1
1
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1
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1
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12
1
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1
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1
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13
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1
1
11
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1
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1
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1
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12
1
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37411
Graham
Inhibition of platelet heparit ...
Homo sapiens
Biochem. Mol. Biol. Int.
37
239-246
1995
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2
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37409
Yamada
Structural studies on the tri- ...
Pedobacter heparinus
Glycobiology
4
69-78
1994
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37410
Suhahara
Structural studies on the olig ...
Pedobacter heparinus
Glycobiology
4
535-544
1994
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37412
Brickman
Heparitinase inhibition of mes ...
Pedobacter heparinus
Dev. Biol.
164
484-501
1994
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1
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37407
Desai
Specificity studies on the hep ...
Pedobacter heparinus
Biochemistry
32
8140-8145
1993
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37406
Nader H.B.; Porcionatto M.A.; Tersariol
Purification and substrate spe ...
Pedobacter heparinus
J. Biol. Chem.
265
16807-16813
1990
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1
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1
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6
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1
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6
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1
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37408
Linhardt
Examination of the substrate s ...
Pedobacter heparinus
Biochemistry
29
2611-2617
1990
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1
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1
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37404
Nader
Heparin sequences in the hepar ...
Pedobacter heparinus
Proc. Natl. Acad. Sci. USA
84
3565-3569
1987
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2
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1
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1
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1
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5978
Hovingh
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5
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1
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5
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3
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1
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1
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1
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1
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