BRENDA - Enzyme Database show
show all sequences of 4.3.3.6

Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii

Matsuura, A.; Yoon, J.Y.; Yoon, H.J.; Lee, H.H.; Suh, S.W.; Mol. Cells 34, 407-412 (2012)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expressed in Escherichia coli Rosetta2 (DE3) pLysS; overexpressed in Escherichia coli strain Rosetta2 (DE3)
Pyrococcus horikoshii
Crystallization (Commentary)
Crystallization
Organism
2-methyl-2,4-pentanediol; crystallized at 23°C using 2-methyl-2,4-pentanediol as a precipitant. Crystals of apo and ribose 5'-phosphate complex forms of PdxS diffract to 2.7 A and 3.1 A resolution, respectively, and belong to the monoclinic space group P2(1)
Pyrococcus horikoshii
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Pyrococcus horikoshii
O59080
-
-
Pyrococcus horikoshii OT-3
O59080
-
-
Purification (Commentary)
Commentary
Organism
-
Pyrococcus horikoshii
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
-
723192
Pyrococcus horikoshii
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
-
723192
Pyrococcus horikoshii OT-3
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
-
-
?
Subunits
Subunits
Commentary
Organism
hexamer
PdxS exists as a hexamer or dodecamer depending on species and makes a 1:1 complex with PdxT. Pyrococcus horikoshii PdxS forms hexamer in solution. It has a 37 amino acids insertion region, which is found in some archaeal PdxS proteins. This additional insertion perturbs dodecamer formation of Pyrococcus horikoshii PdxS
Pyrococcus horikoshii
homohexamer
gel filtration
Pyrococcus horikoshii
Cloned(Commentary) (protein specific)
Commentary
Organism
expressed in Escherichia coli Rosetta2 (DE3) pLysS; overexpressed in Escherichia coli strain Rosetta2 (DE3)
Pyrococcus horikoshii
Crystallization (Commentary) (protein specific)
Crystallization
Organism
2-methyl-2,4-pentanediol; crystallized at 23°C using 2-methyl-2,4-pentanediol as a precipitant. Crystals of apo and ribose 5'-phosphate complex forms of PdxS diffract to 2.7 A and 3.1 A resolution, respectively, and belong to the monoclinic space group P2(1)
Pyrococcus horikoshii
Purification (Commentary) (protein specific)
Commentary
Organism
-
Pyrococcus horikoshii
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
-
723192
Pyrococcus horikoshii
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
-
723192
Pyrococcus horikoshii OT-3
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
hexamer
PdxS exists as a hexamer or dodecamer depending on species and makes a 1:1 complex with PdxT. Pyrococcus horikoshii PdxS forms hexamer in solution. It has a 37 amino acids insertion region, which is found in some archaeal PdxS proteins. This additional insertion perturbs dodecamer formation of Pyrococcus horikoshii PdxS
Pyrococcus horikoshii
homohexamer
gel filtration
Pyrococcus horikoshii
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)
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1
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1
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4
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2
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1
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5
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3
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2
2
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721233
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Pyrococcus horikoshii, Pyrococcus horikoshii OT-3
Acta Crystallogr. Sect. F
68
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2012
-
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1
1
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2
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9
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1
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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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2
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726499
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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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Jochmann
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2
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2
1
1
2
-
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-
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24
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1
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13
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24
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1
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13
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25
25
724219
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6
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724999
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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
1
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7
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1
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714170
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48
1928-1935
2009
-
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1
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10
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2
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1
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10
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713758
Hanes
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Angew. Chem. Int. Ed. Engl.
47
2102-2105
2008
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716306
Hanes
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Nat. Chem. Biol.
4
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2008
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715491
Raschle
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Bacillus subtilis
J. Biol. Chem.
282
6098-6105
2007
-
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5
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2
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3
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1
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2
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4
1
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2
2
716736
Strohmeier
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Bacillus subtilis
Proc. Natl. Acad. Sci. USA
103
19284-19289
2006
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1
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715247
Burns
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Bacillus subtilis
J. Am. Chem. Soc.
127
3682-3683
2005
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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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2