BRENDA - Enzyme Database show
show all sequences of 4.3.3.6

Reaction mechanism of pyridoxal 5'-phosphate synthase. Detection of an enzyme-bound chromophoric intermediate

Raschle, T.; Arigoni, D.; Brunisholz, R.; Rechsteiner, H.; Amrhein, N.; Fitzpatrick, T.B.; J. Biol. Chem. 282, 6098-6105 (2007)

Data extracted from this reference:

Engineering
Amino acid exchange
Commentary
Organism
H170N
catalytically incompetent mutant of glutaminase subunit Pdx2
Bacillus subtilis
K149A
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) does not form the imine adduct
Bacillus subtilis
K149R
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) retains the ability to form the imine adduct
Bacillus subtilis
K81A
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) does not form the imine adduct
Bacillus subtilis
K81R
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) does not form the imine adduct
Bacillus subtilis
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.126
-
D-ribose 5-phosphate
pH 8.0, 37°C, wild-type enzyme
Bacillus subtilis
0.185
-
D-ribose 5-phosphate
pH 8.0, 37°C, mutant enzyme K149R
Bacillus subtilis
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Bacillus subtilis
-
-
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
preference of D-ribose 5-phosphate compared to D-ribulose 5-phosphate. Characterization of a novel chromophoric reaction intermediate. The chromophoric group of this intermediate is appended to the epsilon-amino group of Lys81 and that the new residue has the composition C5H6O2, corresponding to the elimination of one equivalent of inorganic phosphate, one molecule of water one additional proton from the original protonated imine adduct
715491
Bacillus subtilis
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
-
-
-
?
D-ribulose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
preference of D-ribose 5-phosphate compared to D-ribulose 5-phosphate
715491
Bacillus subtilis
?
-
-
-
?
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Bacillus subtilis
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.00033
-
D-ribose 5-phosphate
pH 8.0, 37°C, mutant enzyme K149R
Bacillus subtilis
0.00067
-
D-ribose 5-phosphate
pH 8.0, 37°C, free pyridoxal 5'-phosphate synthase subunit (Pdx1)
Bacillus subtilis
0.0007
-
D-ribulose 5-phosphate
pH 8.0, 37°C, free pyridoxal 5'-phosphate synthase subunit (Pdx1)
Bacillus subtilis
0.004
-
D-ribose 5-phosphate
pH 8.0, 37°C, wild-type enzyme
Bacillus subtilis
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Bacillus subtilis
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
H170N
catalytically incompetent mutant of glutaminase subunit Pdx2
Bacillus subtilis
K149A
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) does not form the imine adduct
Bacillus subtilis
K149R
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) retains the ability to form the imine adduct
Bacillus subtilis
K81A
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) does not form the imine adduct
Bacillus subtilis
K81R
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) does not form the imine adduct
Bacillus subtilis
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.126
-
D-ribose 5-phosphate
pH 8.0, 37°C, wild-type enzyme
Bacillus subtilis
0.185
-
D-ribose 5-phosphate
pH 8.0, 37°C, mutant enzyme K149R
Bacillus subtilis
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
preference of D-ribose 5-phosphate compared to D-ribulose 5-phosphate. Characterization of a novel chromophoric reaction intermediate. The chromophoric group of this intermediate is appended to the epsilon-amino group of Lys81 and that the new residue has the composition C5H6O2, corresponding to the elimination of one equivalent of inorganic phosphate, one molecule of water one additional proton from the original protonated imine adduct
715491
Bacillus subtilis
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
-
-
-
?
D-ribulose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
preference of D-ribose 5-phosphate compared to D-ribulose 5-phosphate
715491
Bacillus subtilis
?
-
-
-
?
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Bacillus subtilis
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.00033
-
D-ribose 5-phosphate
pH 8.0, 37°C, mutant enzyme K149R
Bacillus subtilis
0.00067
-
D-ribose 5-phosphate
pH 8.0, 37°C, free pyridoxal 5'-phosphate synthase subunit (Pdx1)
Bacillus subtilis
0.0007
-
D-ribulose 5-phosphate
pH 8.0, 37°C, free pyridoxal 5'-phosphate synthase subunit (Pdx1)
Bacillus subtilis
0.004
-
D-ribose 5-phosphate
pH 8.0, 37°C, wild-type enzyme
Bacillus subtilis
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Bacillus subtilis
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.0018
-
D-ribose 5-phosphate
pH 8.0, 37°C, mutant enzyme K149R
Bacillus subtilis
0.03
-
D-ribose 5-phosphate
pH 8.0, 37°C, wild-type enzyme
Bacillus subtilis
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.0018
-
D-ribose 5-phosphate
pH 8.0, 37°C, mutant enzyme K149R
Bacillus subtilis
0.03
-
D-ribose 5-phosphate
pH 8.0, 37°C, wild-type enzyme
Bacillus subtilis
Other publictions for EC 4.3.3.6
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)
748203
Smith
Crystal structures capture th ...
Geobacillus kaustophilus
J. Biol. Chem.
290
5226-5239
2015
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1
1
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3
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1
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1
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1
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3
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1
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3
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730418
Belitsky
Role of PdxR in the activation ...
Listeria monocytogenes
Mol. Microbiol.
92
1113-1128
2014
1
-
1
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1
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1
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724239
Reeksting
Exploring inhibition of Pdx1, ...
Plasmodium falciparum
Biochem. J.
449
175-187
2013
-
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1
-
5
-
5
-
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-
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3
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1
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1
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5
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1
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5
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5
5
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1
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1
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729134
Kim
Crystal structure of Mycobacte ...
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
Biochem. Biophys. Res. Commun.
435
255-259
2013
-
1
1
1
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
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4
4
-
-
-
729433
Itagaki
Differences in the roles of a ...
Bacillus circulans, Bacillus circulans SANK 72073, Bacillus subtilis
Biosci. Biotechnol. Biochem.
77
1481-1485
2013
-
-
2
-
1
-
-
-
-
-
-
3
-
5
-
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3
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3
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1
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3
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3
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-
2
2
-
-
-
721233
Yoon
Overexpression, crystallizatio ...
Pyrococcus horikoshii, Pyrococcus horikoshii OT-3
Acta Crystallogr. Sect. F
68
440-442
2012
-
-
1
1
-
-
-
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-
-
2
-
-
9
-
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1
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1
1
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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
-
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-
-
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-
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-
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-
723192
Matsuura
Crystal structure of pyridoxal ...
Pyrococcus horikoshii, Pyrococcus horikoshii OT-3
Mol. Cells
34
407-412
2012
-
-
1
1
-
-
-
-
-
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4
-
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1
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2
2
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1
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2
2
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-
-
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-
726499
Guedez
Assembly of the eukaryotic PLP ...
Plasmodium berghei, Plasmodium falciparum
Structure
20
172-184
2012
-
-
2
2
8
-
-
-
-
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-
4
-
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2
-
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28
-
4
2
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2
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2
8
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2
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28
-
4
2
-
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-
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-
-
-
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-
716150
Jochmann
Positive transcriptional contr ...
Corynebacterium glutamicum, Corynebacterium glutamicum NJ0898
Microbiology
157
77-88
2011
-
-
-
-
-
-
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2
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2
1
1
2
-
-
726269
Moccand
It takes two to Tango: Definin ...
Bacillus subtilis
PLoS ONE
6
e16042
2011
-
-
1
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8
-
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24
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1
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1
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1
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1
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13
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1
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8
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24
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1
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1
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1
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13
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25
25
724219
Zhang
Structural insights into the c ...
Saccharomyces cerevisiae
Biochem. J.
432
445-450
2010
-
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1
1
6
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6
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1
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6
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724999
Derrer
Defining the structural requir ...
Plasmodium falciparum
FEBS Lett.
584
4169-4174
2010
-
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1
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7
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2
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1
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1
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2
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2
1
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1
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7
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1
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2
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2
1
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714170
Wallner
Dissection of contributions fr ...
Bacillus subtilis
Biochemistry
48
1928-1935
2009
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1
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10
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2
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10
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713758
Hanes
Trapping of a chromophoric int ...
Bacillus subtilis
Angew. Chem. Int. Ed. Engl.
47
2102-2105
2008
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716306
Hanes
13C NMR snapshots of the compl ...
Bacillus subtilis
Nat. Chem. Biol.
4
425-430
2008
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715491
Raschle
Reaction mechanism of pyridoxa ...
Bacillus subtilis
J. Biol. Chem.
282
6098-6105
2007
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2
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1
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1
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2
2
716736
Strohmeier
Structure of a bacterial pyrid ...
Bacillus subtilis
Proc. Natl. Acad. Sci. USA
103
19284-19289
2006
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1
1
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1
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715247
Burns
Reconstitution and biochemical ...
Bacillus subtilis
J. Am. Chem. Soc.
127
3682-3683
2005
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1
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1
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715478
Raschle
On the two components of pyrid ...
Bacillus subtilis
J. Biol. Chem.
280
32291-32300
2005
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1
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1
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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1
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1
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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
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4
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1
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2
1
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-
-
2
2