BRENDA - Enzyme Database
show all sequences of 2.5.1.65

Role of F225 in O-phosphoserine sulfhydrylase from Aeropyrum pernix K1

Takeda, E.; Kunimoto, K.; Kawai, Y.; Kataoka, M.; Ishikawa, K.; Nakamura, T.; Extremophiles 20, 733-745 (2016)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
enzyme ApOPSS in complex with aminoacrylate intermediate formed from pyridoxal 5'-phosphate with O-phospho-L-serine or enzyme in complex with L-cysteine, hanging drop vapor diffusion method, mixing of 10 mg/ml protein in 50 mM potassium phosphate, pH 7.5, containing 0.2 mM pyridoxal 5'-phosphate, 2 mM EDTA, and 2 mM TCEP-HCl, with reservoir solutions containing 0.1 M HEPES, pH 7.5, 27% v/v 2-propanol, 10-12% v/v PEG 4000, and 12 mM TCEP-HCl, X-ray diffraction structure determinatoion and analysis at 2.14-2.15 A resolution, structure modeling
Aeropyrum pernix
Engineering
Amino acid exchange
Commentary
Organism
F225A
site-directed mutagenesis, the Km value toward O-phospho-L-serine is not significantly different between the wild-type ApOPSS and the F225A mutant, the kcat value of the wild-type ApOPSS is 4.2fold higher toward O-phospho-L-serine and 15fold higher toward O-acetyl-L-erine than that of the F225A mutant, respectively. The mutation from phenylalanine to alanine at position 225 affects the catalytic activity, not substrate binding
Aeropyrum pernix
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
steady-state kinetics, the Km value toward O-phospho-L-serine is not significantly different between the wild-type ApOPSS and the F225A mutant, the kcat value of the wild-type ApOPSS is 4.2fold higher toward O-phospho-L-serine and 15fold higher toward O-acetyl-L-erine than that of the F225A mutant, respectively
Aeropyrum pernix
0.39
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-acetyl-L-serine
Aeropyrum pernix
1.6
-
hydrogen sulfide
pH 7.5, 80°C, mutant F225A, with O-phospho-L-serine
Aeropyrum pernix
3.8
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-phospho-L-serine
Aeropyrum pernix
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
O-phospho-L-serine + hydrogen sulfide
Aeropyrum pernix
-
L-cysteine + phosphate
-
-
?
O-phospho-L-serine + hydrogen sulfide
Aeropyrum pernix DSM 11879
-
L-cysteine + phosphate
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Aeropyrum pernix
Q9YBL2
-
-
Aeropyrum pernix DSM 11879
Q9YBL2
-
-
Reaction
Reaction
Commentary
Organism
O-phospho-L-serine + hydrogen sulfide = L-cysteine + phosphate
ping-pong bi-bi mechanism, the active site of ApOPSS contains pyridoxal 5'-phosphate linked to lysine 127 as an internal Schiff base. Binding of the primary substrate O-phospho-L-serine displaces the lysine and forms an external Schiff base, initiating the first half-reaction that yields an alpha-aminoacrylate intermediate linked to pyridoxal 5'-phosphate. The second half-reaction involves the addition of a secondary substrate to the alpha-aminoacrylate intermediate and generates an external Schiff base with cysteine. The active-site lysine reacts with this external Schiff base, releasing cysteine and regenerating the internal Schiff base with K127. When other nucleophiles are used instead of sulfide, enzyme ApOPSS produces the corresponding non-natural amino acid
Aeropyrum pernix
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
the enzyme is also active with O-acetyl-L-serine, cf. EC 2.5.1.47. When other nucleophiles are used instead of sulfide, enzyme ApOPSS produces the corresponding non-natural amino acid, when thiosulfate is used as nucleophile, for example, S-sulfocysteine is produced. In absence of sulfide, the primary substrate reacts with to pyridoxal 5'-phosphate in enzyme OPSS to yield an alpha-aminoacrylate intermediate, which is formed through an external Schiff base with the elimination of phosphate or acetate, the intermediate is finally degraded to pyruvate and pyridoxal 5'-phosphate by a water molecule without a nucleophile
738193
Aeropyrum pernix
?
-
-
-
-
additional information
the enzyme is also active with O-acetyl-L-serine, cf. EC 2.5.1.47. When other nucleophiles are used instead of sulfide, enzyme ApOPSS produces the corresponding non-natural amino acid, when thiosulfate is used as nucleophile, for example, S-sulfocysteine is produced. In absence of sulfide, the primary substrate reacts with to pyridoxal 5'-phosphate in enzyme OPSS to yield an alpha-aminoacrylate intermediate, which is formed through an external Schiff base with the elimination of phosphate or acetate, the intermediate is finally degraded to pyruvate and pyridoxal 5'-phosphate by a water molecule without a nucleophile
738193
Aeropyrum pernix DSM 11879
?
-
-
-
-
O-acetyl-L-serine + hydrogen sulfide
low activity
738193
Aeropyrum pernix
L-cysteine + acetate
-
-
-
?
O-acetyl-L-serine + hydrogen sulfide
low activity
738193
Aeropyrum pernix DSM 11879
L-cysteine + acetate
-
-
-
?
O-phospho-L-serine + hydrogen sulfide
-
738193
Aeropyrum pernix
L-cysteine + phosphate
-
-
-
?
O-phospho-L-serine + hydrogen sulfide
best substrate
738193
Aeropyrum pernix
L-cysteine + phosphate
-
-
-
?
O-phospho-L-serine + hydrogen sulfide
-
738193
Aeropyrum pernix DSM 11879
L-cysteine + phosphate
-
-
-
?
O-phospho-L-serine + hydrogen sulfide
best substrate
738193
Aeropyrum pernix DSM 11879
L-cysteine + phosphate
-
-
-
?
O-phospho-L-serine + thiosulfate
-
738193
Aeropyrum pernix
S-sulfocysteine + phosphate
-
-
-
?
O-phospho-L-serine + thiosulfate
-
738193
Aeropyrum pernix DSM 11879
S-sulfocysteine + phosphate
-
-
-
?
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
80
-
assay at
Aeropyrum pernix
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
2.6
-
O-acetyl-L-serine
pH 7.5, 80°C, mutant F225A
Aeropyrum pernix
33
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-acetyl-L-serine
Aeropyrum pernix
38
-
O-acetyl-L-serine
pH 7.5, 80°C, wild-type enzyme
Aeropyrum pernix
130
-
hydrogen sulfide
pH 7.5, 80°C, mutant F225A, with O-phospho-L-serine
Aeropyrum pernix
150
-
O-phospho-L-serine
pH 7.5, 80°C, mutant F225A
Aeropyrum pernix
630
-
O-phospho-L-serine
pH 7.5, 80°C, wild-type enzyme
Aeropyrum pernix
730
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-phospho-L-serine
Aeropyrum pernix
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Aeropyrum pernix
Cofactor
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
linked to lysine K127 as an internal Schiff base at the active site
Aeropyrum pernix
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
linked to lysine K127 as an internal Schiff base at the active site
Aeropyrum pernix
Crystallization (Commentary) (protein specific)
Crystallization
Organism
enzyme ApOPSS in complex with aminoacrylate intermediate formed from pyridoxal 5'-phosphate with O-phospho-L-serine or enzyme in complex with L-cysteine, hanging drop vapor diffusion method, mixing of 10 mg/ml protein in 50 mM potassium phosphate, pH 7.5, containing 0.2 mM pyridoxal 5'-phosphate, 2 mM EDTA, and 2 mM TCEP-HCl, with reservoir solutions containing 0.1 M HEPES, pH 7.5, 27% v/v 2-propanol, 10-12% v/v PEG 4000, and 12 mM TCEP-HCl, X-ray diffraction structure determinatoion and analysis at 2.14-2.15 A resolution, structure modeling
Aeropyrum pernix
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
F225A
site-directed mutagenesis, the Km value toward O-phospho-L-serine is not significantly different between the wild-type ApOPSS and the F225A mutant, the kcat value of the wild-type ApOPSS is 4.2fold higher toward O-phospho-L-serine and 15fold higher toward O-acetyl-L-erine than that of the F225A mutant, respectively. The mutation from phenylalanine to alanine at position 225 affects the catalytic activity, not substrate binding
Aeropyrum pernix
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
steady-state kinetics, the Km value toward O-phospho-L-serine is not significantly different between the wild-type ApOPSS and the F225A mutant, the kcat value of the wild-type ApOPSS is 4.2fold higher toward O-phospho-L-serine and 15fold higher toward O-acetyl-L-erine than that of the F225A mutant, respectively
Aeropyrum pernix
0.39
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-acetyl-L-serine
Aeropyrum pernix
1.6
-
hydrogen sulfide
pH 7.5, 80°C, mutant F225A, with O-phospho-L-serine
Aeropyrum pernix
3.8
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-phospho-L-serine
Aeropyrum pernix
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
O-phospho-L-serine + hydrogen sulfide
Aeropyrum pernix
-
L-cysteine + phosphate
-
-
?
O-phospho-L-serine + hydrogen sulfide
Aeropyrum pernix DSM 11879
-
L-cysteine + phosphate
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
the enzyme is also active with O-acetyl-L-serine, cf. EC 2.5.1.47. When other nucleophiles are used instead of sulfide, enzyme ApOPSS produces the corresponding non-natural amino acid, when thiosulfate is used as nucleophile, for example, S-sulfocysteine is produced. In absence of sulfide, the primary substrate reacts with to pyridoxal 5'-phosphate in enzyme OPSS to yield an alpha-aminoacrylate intermediate, which is formed through an external Schiff base with the elimination of phosphate or acetate, the intermediate is finally degraded to pyruvate and pyridoxal 5'-phosphate by a water molecule without a nucleophile
738193
Aeropyrum pernix
?
-
-
-
-
additional information
the enzyme is also active with O-acetyl-L-serine, cf. EC 2.5.1.47. When other nucleophiles are used instead of sulfide, enzyme ApOPSS produces the corresponding non-natural amino acid, when thiosulfate is used as nucleophile, for example, S-sulfocysteine is produced. In absence of sulfide, the primary substrate reacts with to pyridoxal 5'-phosphate in enzyme OPSS to yield an alpha-aminoacrylate intermediate, which is formed through an external Schiff base with the elimination of phosphate or acetate, the intermediate is finally degraded to pyruvate and pyridoxal 5'-phosphate by a water molecule without a nucleophile
738193
Aeropyrum pernix DSM 11879
?
-
-
-
-
O-acetyl-L-serine + hydrogen sulfide
low activity
738193
Aeropyrum pernix
L-cysteine + acetate
-
-
-
?
O-acetyl-L-serine + hydrogen sulfide
low activity
738193
Aeropyrum pernix DSM 11879
L-cysteine + acetate
-
-
-
?
O-phospho-L-serine + hydrogen sulfide
-
738193
Aeropyrum pernix
L-cysteine + phosphate
-
-
-
?
O-phospho-L-serine + hydrogen sulfide
best substrate
738193
Aeropyrum pernix
L-cysteine + phosphate
-
-
-
?
O-phospho-L-serine + hydrogen sulfide
-
738193
Aeropyrum pernix DSM 11879
L-cysteine + phosphate
-
-
-
?
O-phospho-L-serine + hydrogen sulfide
best substrate
738193
Aeropyrum pernix DSM 11879
L-cysteine + phosphate
-
-
-
?
O-phospho-L-serine + thiosulfate
-
738193
Aeropyrum pernix
S-sulfocysteine + phosphate
-
-
-
?
O-phospho-L-serine + thiosulfate
-
738193
Aeropyrum pernix DSM 11879
S-sulfocysteine + phosphate
-
-
-
?
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
80
-
assay at
Aeropyrum pernix
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
2.6
-
O-acetyl-L-serine
pH 7.5, 80°C, mutant F225A
Aeropyrum pernix
33
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-acetyl-L-serine
Aeropyrum pernix
38
-
O-acetyl-L-serine
pH 7.5, 80°C, wild-type enzyme
Aeropyrum pernix
130
-
hydrogen sulfide
pH 7.5, 80°C, mutant F225A, with O-phospho-L-serine
Aeropyrum pernix
150
-
O-phospho-L-serine
pH 7.5, 80°C, mutant F225A
Aeropyrum pernix
630
-
O-phospho-L-serine
pH 7.5, 80°C, wild-type enzyme
Aeropyrum pernix
730
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-phospho-L-serine
Aeropyrum pernix
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Aeropyrum pernix
General Information
General Information
Commentary
Organism
additional information
three-dimensional structure analysis of enzyme ApOPSS in complex with aminoacrylate intermediate formed from pyridoxal 5'-phosphate with O-phospho-L-serine or the enzyme in complex with L-cysteine, and structure comparisons, molecular docking simulation using the structure of PDB ID 3VSA as the wild-type enzyme ApOPSS, overview
Aeropyrum pernix
General Information (protein specific)
General Information
Commentary
Organism
additional information
three-dimensional structure analysis of enzyme ApOPSS in complex with aminoacrylate intermediate formed from pyridoxal 5'-phosphate with O-phospho-L-serine or the enzyme in complex with L-cysteine, and structure comparisons, molecular docking simulation using the structure of PDB ID 3VSA as the wild-type enzyme ApOPSS, overview
Aeropyrum pernix
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.07
-
O-acetyl-L-serine
pH 7.5, 80°C, mutant F225A
Aeropyrum pernix
2.3
-
O-phospho-L-serine
pH 7.5, 80°C, mutant F225A
Aeropyrum pernix
3.5
-
O-acetyl-L-serine
pH 7.5, 80°C, wild-type enzyme
Aeropyrum pernix
11
-
O-phospho-L-serine
pH 7.5, 80°C, wild-type enzyme
Aeropyrum pernix
81
-
hydrogen sulfide
pH 7.5, 80°C, mutant F225A, with O-phospho-L-serine
Aeropyrum pernix
85
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-acetyl-L-serine
Aeropyrum pernix
190
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-phospho-L-serine
Aeropyrum pernix
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.07
-
O-acetyl-L-serine
pH 7.5, 80°C, mutant F225A
Aeropyrum pernix
2.3
-
O-phospho-L-serine
pH 7.5, 80°C, mutant F225A
Aeropyrum pernix
3.5
-
O-acetyl-L-serine
pH 7.5, 80°C, wild-type enzyme
Aeropyrum pernix
11
-
O-phospho-L-serine
pH 7.5, 80°C, wild-type enzyme
Aeropyrum pernix
81
-
hydrogen sulfide
pH 7.5, 80°C, mutant F225A, with O-phospho-L-serine
Aeropyrum pernix
85
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-acetyl-L-serine
Aeropyrum pernix
190
-
hydrogen sulfide
pH 7.5, 80°C, wild-type enzyme, with O-phospho-L-serine
Aeropyrum pernix
Other publictions for EC 2.5.1.65
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)
738193
Takeda
Role of F225 in O-phosphoserin ...
Aeropyrum pernix, Aeropyrum pernix DSM 11879
Extremophiles
20
733-745
2016
-
-
-
1
1
-
-
4
-
-
-
2
-
5
-
-
-
1
-
-
-
-
10
-
1
-
-
7
1
-
-
1
-
-
-
-
-
-
1
1
1
-
-
-
-
4
-
-
-
2
-
-
-
-
-
-
-
-
10
-
1
-
-
7
1
-
-
-
-
1
1
-
7
7
737868
Nakamura
Thermostability and reactivity ...
Aeropyrum pernix, Aeropyrum pernix DSM 11879
Biosci. Biotechnol. Biochem.
79
1280-1286
2015
-
-
1
-
-
-
-
-
-
-
-
2
2
6
-
-
1
1
-
-
-
-
6
-
1
-
1
-
1
-
-
1
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
2
2
-
-
1
-
-
-
-
6
-
1
-
1
-
1
-
-
-
-
1
1
-
-
-
738534
Steiner
CysK2 from Mycobacterium tuber ...
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
J. Bacteriol.
196
3410-3420
2014
-
-
1
-
2
-
-
8
-
-
-
2
-
3
-
-
1
1
-
-
-
-
6
1
1
-
-
4
2
-
-
1
-
-
-
-
-
1
1
-
2
-
-
-
-
8
-
-
-
2
-
-
-
1
-
-
-
-
6
1
1
-
-
4
2
-
-
-
-
2
2
-
5
5
722990
Nakamura
Structural analysis of the sub ...
Aeropyrum pernix
J. Mol. Biol.
422
33-44
2012
-
-
1
1
11
-
-
-
-
-
-
-
-
4
-
-
-
-
-
-
1
-
2
-
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
1
11
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
685195
OLeary
O-Phospho-l-serine and the thi ...
Mycobacterium tuberculosis
Biochemistry
47
11606-11615
2008
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
3
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
3
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
687773
Agren
Cysteine synthase (CYSM) of My ...
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
J. Biol. Chem.
283
31567-31574
2008
-
-
1
1
1
-
-
-
-
-
-
4
-
6
-
-
1
-
-
-
-
-
8
-
-
-
-
1
-
-
-
1
-
-
-
-
-
2
2
2
2
-
-
-
-
-
-
-
-
4
-
-
-
1
-
-
-
-
8
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
702213
Jurgenson
Crystal structure of a sulfur ...
Mycobacterium tuberculosis
Biochemistry
47
10354-10364
2008
-
-
1
1
1
-
-
-
-
-
-
-
-
1
-
-
1
-
-
-
-
-
-
1
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
1
1
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
-
-
-
-
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659728
Oda
Three-dimensional structure of ...
Aeropyrum pernix
J. Mol. Biol.
351
334-344
2005
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7
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4
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4
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4
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637385
Mino
Characterization of a novel th ...
Aeropyrum pernix
J. Bacteriol.
185
2277-2284
2003
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4
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654085
Mino
Crystallization and preliminar ...
Aeropyrum pernix
Acta Crystallogr. Sect. D
59
338-340
2003
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1
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655576
Mino
A novel O-phospho-L-serine sul ...
Aeropyrum pernix
FEBS Lett.
551
133-138
2003
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23
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