BRENDA - Enzyme Database
show all sequences of 6.3.2.9

Role of the ortholog and paralog amino acid invariants in the active site of the UDP-MurNAc-L-alanine:D-glutamate ligase (MurD)

Bouhss, A.; Dementin, S.; Parquet, C.; Mengin-Lecreulx, D.; Bertrand, J.A.; Le Beller, D.; Dideberg, O.; van Heijenoort, J.; Blanot, D.; Biochemistry 38, 12240-12247 (1999)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expressed in Escherichia coli
Escherichia coli
Engineering
Amino acid exchange
Commentary
Organism
D317A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
D35A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
E157A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
E157K
reduced enzymatic activity with respect to the wild-type
Escherichia coli
H183A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
H301A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
K115A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
K198A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
K198F
reduced enzymatic activity with respect to the wild-type
Escherichia coli
N268A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
N271A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
R302A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
R425A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
Y194F
reduced enzymatic activity with respect to the wild-type
Escherichia coli
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.012
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, N268A mutant protein
Escherichia coli
0.016
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, N271A mutant protein
Escherichia coli
0.03
-
ATP
pH 9.4, 37°C, E157A mutant protein
Escherichia coli
0.04
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, H301A mutant protein
Escherichia coli
0.044
-
D-glutamate
pH 9.4, 37°C, D317A mutant protein
Escherichia coli
0.046
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, K115A mutant protein
Escherichia coli
0.053
-
D-glutamate
pH 9.4, 37°C, N271A mutant protein; pH 9.4, 37°C, Y194F mutant protein
Escherichia coli
0.053
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, R425A mutant protein
Escherichia coli
0.056
-
D-glutamate
pH 9.4, 37°C, E157K mutant protein
Escherichia coli
0.057
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, D317A mutant protein
Escherichia coli
0.059
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, H183A mutant protein
Escherichia coli
0.065
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, R302A mutant protein
Escherichia coli
0.074
-
D-glutamate
pH 9.4, 37°C, R302A mutant protein
Escherichia coli
0.084
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, D35A mutant protein
Escherichia coli
0.085
-
ATP
pH 9.4, 37°C, E157K mutant protein
Escherichia coli
0.095
-
D-glutamate
pH 9.4, 37°C, D35A mutant protein; pH 9.4, 37°C, H301A mutant protein
Escherichia coli
0.111
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, Y194F mutant protein
Escherichia coli
0.114
-
ATP
pH 9.4, 37°C, D35A mutant protein
Escherichia coli
0.12
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, K198A mutant protein
Escherichia coli
0.128
-
D-glutamate
pH 9.4, 37°C, K115A mutant protein
Escherichia coli
0.129
-
ATP
pH 9.4, 37°C, K198F mutant protein
Escherichia coli
0.13
-
ATP
pH 9.4, 37°C, H183A mutant protein
Escherichia coli
0.135
-
ATP
pH 9.4, 37°C, K198A mutant protein
Escherichia coli
0.14
-
ATP
pH 9.4, 37°C, N268A mutant protein
Escherichia coli
0.14
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, K198F mutant protein
Escherichia coli
0.144
-
ATP
pH 9.4, 37°C, Y194F mutant protein
Escherichia coli
0.153
-
ATP
pH 9.4, 37°C, H301A mutant protein
Escherichia coli
0.183
-
ATP
pH 9.4, 37°C, R425A mutant protein
Escherichia coli
0.185
-
D-glutamate
pH 9.4, 37°C, K198A mutant protein
Escherichia coli
0.216
-
D-glutamate
pH 9.4, 37°C, K198F mutant protein
Escherichia coli
0.218
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, E157K mutant protein
Escherichia coli
0.264
-
D-glutamate
pH 9.4, 37°C, N268A mutant protein
Escherichia coli
0.304
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, E157A mutant protein
Escherichia coli
0.328
-
ATP
pH 9.4, 37°C, K115A mutant protein
Escherichia coli
0.806
-
D-glutamate
pH 9.4, 37°C, H183A mutant protein
Escherichia coli
1.58
-
ATP
pH 9.4, 37°C, N271A mutant protein
Escherichia coli
2
-
ATP
pH 9.4, 37°C, R302A mutant protein
Escherichia coli
2.18
-
ATP
pH 9.4, 37°C, D317A mutant protein
Escherichia coli
5.16
-
D-glutamate
pH 9.4, 37°C, R425A mutant protein
Escherichia coli
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
-
strain DH5alpha
-
Escherichia coli DH5-alpha
-
strain DH5alpha
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ATP + UDP-N-acetylmuramate-L-alanine + D-glutamate
-
649861
Escherichia coli
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
649861
Escherichia coli
r
ATP + UDP-N-acetylmuramate-L-alanine + D-glutamate
-
649861
Escherichia coli DH5-alpha
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
649861
Escherichia coli DH5-alpha
r
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.0003
-
D-glutamate
pH 9.4, 37°C, E157K mutant protein
Escherichia coli
0.0004
-
D-glutamate
pH 9.4, 37°C, H183A mutant protein
Escherichia coli
0.004
-
D-glutamate
pH 9.4, 37°C, K115A mutant protein
Escherichia coli
0.012
-
D-glutamate
pH 9.4, 37°C, K198F mutant protein
Escherichia coli
0.016
-
D-glutamate
pH 9.4, 37°C, K198A mutant protein
Escherichia coli
0.022
-
D-glutamate
pH 9.4, 37°C, D317A mutant protein
Escherichia coli
0.093
-
D-glutamate
pH 9.4, 37°C, Y194F mutant protein
Escherichia coli
0.3
-
D-glutamate
pH 9.4, 37°C, N271A mutant protein
Escherichia coli
0.53
-
D-glutamate
pH 9.4, 37°C, R425A mutant protein
Escherichia coli
0.77
-
D-glutamate
pH 9.4, 37°C, H301A mutant protein
Escherichia coli
3
6
D-glutamate
pH 9.4, 37°C, R302A mutant protein
Escherichia coli
3.13
-
D-glutamate
pH 9.4, 37°C, D35A mutant protein; pH 9.4, 37°C, R302A mutant protein
Escherichia coli
3.3
-
D-glutamate
pH 9.4, 37°C, N268A mutant protein
Escherichia coli
4.27
-
D-glutamate
pH 9.4, 37°C, D35A mutant protein
Escherichia coli
5.12
-
D-glutamate
pH 9.4, 37°C, N268A mutant protein
Escherichia coli
6.08
-
D-glutamate
pH 9.4, 37°C, H301A mutant protein; pH 9.4, 37°C, R425A mutant protein
Escherichia coli
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
9.4
-
-
Escherichia coli
Cloned(Commentary) (protein specific)
Commentary
Organism
expressed in Escherichia coli
Escherichia coli
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
D317A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
D35A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
E157A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
E157K
reduced enzymatic activity with respect to the wild-type
Escherichia coli
H183A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
H301A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
K115A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
K198A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
K198F
reduced enzymatic activity with respect to the wild-type
Escherichia coli
N268A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
N271A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
R302A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
R425A
reduced enzymatic activity with respect to the wild-type
Escherichia coli
Y194F
reduced enzymatic activity with respect to the wild-type
Escherichia coli
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.012
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, N268A mutant protein
Escherichia coli
0.016
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, N271A mutant protein
Escherichia coli
0.03
-
ATP
pH 9.4, 37°C, E157A mutant protein
Escherichia coli
0.04
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, H301A mutant protein
Escherichia coli
0.044
-
D-glutamate
pH 9.4, 37°C, D317A mutant protein
Escherichia coli
0.046
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, K115A mutant protein
Escherichia coli
0.053
-
D-glutamate
pH 9.4, 37°C, N271A mutant protein; pH 9.4, 37°C, Y194F mutant protein
Escherichia coli
0.053
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, R425A mutant protein
Escherichia coli
0.056
-
D-glutamate
pH 9.4, 37°C, E157K mutant protein
Escherichia coli
0.057
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, D317A mutant protein
Escherichia coli
0.059
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, H183A mutant protein
Escherichia coli
0.065
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, R302A mutant protein
Escherichia coli
0.074
-
D-glutamate
pH 9.4, 37°C, R302A mutant protein
Escherichia coli
0.084
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, D35A mutant protein
Escherichia coli
0.085
-
ATP
pH 9.4, 37°C, E157K mutant protein
Escherichia coli
0.095
-
D-glutamate
pH 9.4, 37°C, D35A mutant protein; pH 9.4, 37°C, H301A mutant protein
Escherichia coli
0.111
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, Y194F mutant protein
Escherichia coli
0.114
-
ATP
pH 9.4, 37°C, D35A mutant protein
Escherichia coli
0.12
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, K198A mutant protein
Escherichia coli
0.128
-
D-glutamate
pH 9.4, 37°C, K115A mutant protein
Escherichia coli
0.129
-
ATP
pH 9.4, 37°C, K198F mutant protein
Escherichia coli
0.13
-
ATP
pH 9.4, 37°C, H183A mutant protein
Escherichia coli
0.135
-
ATP
pH 9.4, 37°C, K198A mutant protein
Escherichia coli
0.14
-
ATP
pH 9.4, 37°C, N268A mutant protein
Escherichia coli
0.14
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, K198F mutant protein
Escherichia coli
0.144
-
ATP
pH 9.4, 37°C, Y194F mutant protein
Escherichia coli
0.153
-
ATP
pH 9.4, 37°C, H301A mutant protein
Escherichia coli
0.183
-
ATP
pH 9.4, 37°C, R425A mutant protein
Escherichia coli
0.185
-
D-glutamate
pH 9.4, 37°C, K198A mutant protein
Escherichia coli
0.216
-
D-glutamate
pH 9.4, 37°C, K198F mutant protein
Escherichia coli
0.218
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, E157K mutant protein
Escherichia coli
0.264
-
D-glutamate
pH 9.4, 37°C, N268A mutant protein
Escherichia coli
0.304
-
UDP-N-acetylmuramoyl L-alanine
pH 9.4, 37°C, E157A mutant protein
Escherichia coli
0.328
-
ATP
pH 9.4, 37°C, K115A mutant protein
Escherichia coli
0.806
-
D-glutamate
pH 9.4, 37°C, H183A mutant protein
Escherichia coli
1.58
-
ATP
pH 9.4, 37°C, N271A mutant protein
Escherichia coli
2
-
ATP
pH 9.4, 37°C, R302A mutant protein
Escherichia coli
2.18
-
ATP
pH 9.4, 37°C, D317A mutant protein
Escherichia coli
5.16
-
D-glutamate
pH 9.4, 37°C, R425A mutant protein
Escherichia coli
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ATP + UDP-N-acetylmuramate-L-alanine + D-glutamate
-
649861
Escherichia coli
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
649861
Escherichia coli
r
ATP + UDP-N-acetylmuramate-L-alanine + D-glutamate
-
649861
Escherichia coli DH5-alpha
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
-
649861
Escherichia coli DH5-alpha
r
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.0003
-
D-glutamate
pH 9.4, 37°C, E157K mutant protein
Escherichia coli
0.0004
-
D-glutamate
pH 9.4, 37°C, H183A mutant protein
Escherichia coli
0.004
-
D-glutamate
pH 9.4, 37°C, K115A mutant protein
Escherichia coli
0.012
-
D-glutamate
pH 9.4, 37°C, K198F mutant protein
Escherichia coli
0.016
-
D-glutamate
pH 9.4, 37°C, K198A mutant protein
Escherichia coli
0.022
-
D-glutamate
pH 9.4, 37°C, D317A mutant protein
Escherichia coli
0.093
-
D-glutamate
pH 9.4, 37°C, Y194F mutant protein
Escherichia coli
0.3
-
D-glutamate
pH 9.4, 37°C, N271A mutant protein
Escherichia coli
0.53
-
D-glutamate
pH 9.4, 37°C, R425A mutant protein
Escherichia coli
0.77
-
D-glutamate
pH 9.4, 37°C, H301A mutant protein
Escherichia coli
3
6
D-glutamate
pH 9.4, 37°C, R302A mutant protein
Escherichia coli
3.13
-
D-glutamate
pH 9.4, 37°C, D35A mutant protein; pH 9.4, 37°C, R302A mutant protein
Escherichia coli
3.3
-
D-glutamate
pH 9.4, 37°C, N268A mutant protein
Escherichia coli
4.27
-
D-glutamate
pH 9.4, 37°C, D35A mutant protein
Escherichia coli
5.12
-
D-glutamate
pH 9.4, 37°C, N268A mutant protein
Escherichia coli
6.08
-
D-glutamate
pH 9.4, 37°C, H301A mutant protein; pH 9.4, 37°C, R425A mutant protein
Escherichia coli
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
9.4
-
-
Escherichia coli
Other publictions for EC 6.3.2.9
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)
746203
Sink
Crystallographic study of pept ...
Escherichia coli
PLoS ONE
11
e0152075
2016
-
1
1
1
-
-
-
1
1
1
-
-
-
1
-
-
1
1
-
-
-
-
2
-
-
-
-
-
-
-
-
1
-
-
-
-
1
1
1
1
-
-
-
-
-
1
1
1
-
-
-
-
-
1
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
3
3
-
-
-
715974
Tomasic
Virtual screening for potentia ...
Escherichia coli
J. Mol. Model.
18
1063-1072
2012
-
-
-
-
-
-
4
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
714902
Sosic
Second-generation sulfonamide ...
Escherichia coli
Eur. J. Med. Chem.
46
2880-2894
2011
-
-
-
1
-
-
4
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
4
-
4
-
-
-
-
1
-
-
4
4
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
714905
Tomasic
Novel 2-thioxothiazolidin-4-on ...
Escherichia coli
Eur. J. Med. Chem.
46
3964-3975
2011
-
-
-
-
-
-
3
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
3
3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
715866
Tomasic
Structure-based design of a ne ...
Escherichia coli
J. Med. Chem.
54
4600-4610
2011
-
-
-
1
-
-
5
-
-
-
-
-
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
5
-
-
-
-
1
-
-
5
5
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
714367
Patin
Purification and biochemical c ...
Staphylococcus aureus
Biochimie
92
1793-1800
2010
-
-
1
-
-
-
-
3
-
1
-
-
-
1
-
-
1
-
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
3
-
1
-
-
-
-
-
1
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
715722
Umamaheswari
-
Virtual screening for potentia ...
Leptospira interrogans
J. Chem. Biol.
13
175-187
2010
-
-
-
1
-
-
1
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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NMR and molecular dynamics stu ...
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Frlan
Design and synthesis of novel ...
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Perdih
MurD ligase from E. coli: Tetr ...
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2008
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Determination of the MurD mech ...
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Large-scale preparation, purif ...
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3
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1
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1
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3
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1
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1
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1
1
4
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2
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2
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2
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1
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1
1
4
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1275
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2
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2
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