BRENDA - Enzyme Database
show all sequences of 6.3.2.49

Crystallization and preliminary X-ray diffraction analysis of Bacillus subtilis YwfE, an L-amino-acid ligase

Tsuda, T.; Suzuki, T.; Kojima, S.; Acta Crystallogr. Sect. F 68, 203-206 (2012)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
purified wild-type and selenomethionine-labeled YwfE in complex with ADP, MgCl2 and dipeptide L-Ala-L-Gln, hanging drop vapour diffusion method, mixing of 0.002 ml of protein solution containing 8 mg/ml protein, 10 mM ADP, 10 mM MgCl2, 100 mM L-Ala-L-Gln with 0.002 ml reservoir solution, equilibration against 0.5 ml of reservoir solution, the deletion-mutant crystals are grown in reservoir solution consisting of 17% w/v PEG 3350, 0.3 M NaCl, 0.1 M MES-NaOH, pH 6.75, 5% v/v ethylene glycol, 1 mM DTT, X-ray diffraction structure determination and analysis at 1.9 A and 2.8 A, respectively
Bacillus subtilis
Engineering
Amino acid exchange
Commentary
Organism
additional information
generation of a deletion mutant comprising residues Lys4-Tyr468
Bacillus subtilis
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
55000
-
2 * 55000, SDS-PAGE
Bacillus subtilis
105000
-
gel filtration
Bacillus subtilis
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Bacillus subtilis
P39641
-
-
Bacillus subtilis 168
P39641
-
-
Purification (Commentary)
Commentary
Organism
recombinant N-terminally GST-tagged wild-type and mutant enzymes (deletion mutant comprising residues Lys4-Tyr468) from Escherichia coli strain ArcticExpress RIL cells (DE3) by glutathione affinity chromatography, tag cleavage by PreScission protease, dialysis and removal of the tag by glutathione affinity chromatography, followed by ultrafiltration and gel filtration, recombinant selenomethionine-labeled enzyme from Escherichia coli strain B834(DE3) purified by the same procedure
Bacillus subtilis
Subunits
Subunits
Commentary
Organism
dimer
2 * 55000, SDS-PAGE
Bacillus subtilis
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified wild-type and selenomethionine-labeled YwfE in complex with ADP, MgCl2 and dipeptide L-Ala-L-Gln, hanging drop vapour diffusion method, mixing of 0.002 ml of protein solution containing 8 mg/ml protein, 10 mM ADP, 10 mM MgCl2, 100 mM L-Ala-L-Gln with 0.002 ml reservoir solution, equilibration against 0.5 ml of reservoir solution, the deletion-mutant crystals are grown in reservoir solution consisting of 17% w/v PEG 3350, 0.3 M NaCl, 0.1 M MES-NaOH, pH 6.75, 5% v/v ethylene glycol, 1 mM DTT, X-ray diffraction structure determination and analysis at 1.9 A and 2.8 A, respectively
Bacillus subtilis
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
additional information
generation of a deletion mutant comprising residues Lys4-Tyr468
Bacillus subtilis
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
55000
-
2 * 55000, SDS-PAGE
Bacillus subtilis
105000
-
gel filtration
Bacillus subtilis
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant N-terminally GST-tagged wild-type and mutant enzymes (deletion mutant comprising residues Lys4-Tyr468) from Escherichia coli strain ArcticExpress RIL cells (DE3) by glutathione affinity chromatography, tag cleavage by PreScission protease, dialysis and removal of the tag by glutathione affinity chromatography, followed by ultrafiltration and gel filtration, recombinant selenomethionine-labeled enzyme from Escherichia coli strain B834(DE3) purified by the same procedure
Bacillus subtilis
Subunits (protein specific)
Subunits
Commentary
Organism
dimer
2 * 55000, SDS-PAGE
Bacillus subtilis
Other publictions for EC 6.3.2.49
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)
733347
Tsuda
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53
2650-2660
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-
1
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1
1
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-
-
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1
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2
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3
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1
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1
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1
1
1
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1
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3
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2
2
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726743
Arai
L-amino acid ligase from Pseud ...
Pseudomonas syringae, Pseudomonas syringae NBRC 14081
Appl. Environ. Microbiol.
79
5023-5029
2013
-
1
1
-
-
-
-
-
-
1
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4
-
4
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-
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-
-
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100
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1
1
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-
1
1
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1
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1
1
1
-
-
-
-
-
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-
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1
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4
-
-
-
-
-
-
-
-
100
-
1
1
-
-
1
1
-
-
-
-
-
-
-
-
729244
Parker
Action and timing of BacC and ...
Bacillus subtilis 168, Bacillus subtilis
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889-901
2013
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-
1
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-
-
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2
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6
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1
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8
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1
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1
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8
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
726581
Suzuki
The structure of L-amino-acid ...
Bacillus licheniformis, Bacillus licheniformis NBRC 12200
Acta Crystallogr. Sect. D
68
1535-1540
2012
-
-
1
1
-
-
-
-
-
1
-
2
-
4
-
-
1
-
-
-
-
-
4
-
-
-
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-
-
-
-
1
-
-
-
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1
1
1
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-
-
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1
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2
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-
1
-
-
-
-
4
-
-
-
-
-
-
-
-
-
-
2
2
-
-
-
726615
Tsuda
Crystallization and preliminar ...
Bacillus subtilis 168, Bacillus subtilis
Acta Crystallogr. Sect. F
68
203-206
2012
-
-
-
1
1
-
-
-
-
-
2
-
-
7
-
-
1
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
1
1
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-
-
-
-
-
-
2
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
730896
Shomura
Structural and enzymatic chara ...
Bacillus subtilis 168, Bacillus subtilis
Protein Sci.
21
707-716
2012
-
1
1
1
2
-
1
12
-
-
-
2
-
6
-
-
1
-
-
-
-
-
6
1
1
-
-
10
1
-
-
-
1
-
-
-
1
1
-
1
2
-
-
1
1
12
-
-
-
2
-
-
-
1
-
-
-
-
6
1
1
-
-
10
1
-
-
-
-
-
-
-
-
-
702768
Kino
A novel L-amino acid ligase fr ...
Bacillus subtilis, Bacillus subtilis NBRC3134
Biosci. Biotechnol. Biochem.
74
129-134
2010
-
-
1
-
-
-
-
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1
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-
4
-
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2
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1
1
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1
1
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1
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-
-
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1
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-
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-
-
2
-
1
1
-
-
1
1
-
-
-
1
1
-
-
-
702771
Senoo
Identification of novel L-amin ...
Actinobacillus pleuropneumoniae, Photorhabdus laumondii subsp. laumondii, Streptococcus mutans, Streptococcus pneumoniae, Treponema denticola
Biosci. Biotechnol. Biochem.
74
415-418
2010
-
-
5
-
-
-
-
-
-
-
-
-
-
5
-
-
5
-
-
-
-
-
115
-
5
-
-
-
5
-
-
-
-
-
-
-
-
5
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
5
-
-
-
-
115
-
5
-
-
-
5
-
-
-
-
-
-
-
-
-
690733
Kino
Dipeptide synthesis by L-amino ...
Ralstonia solanacearum, Ralstonia solanacearum JCM 10489
Biochem. Biophys. Res. Commun.
371
536-540
2008
-
-
1
-
-
-
-
1
-
1
1
2
-
4
-
-
1
-
-
-
-
-
4
1
1
-
-
-
1
1
-
1
-
-
-
-
-
1
1
-
-
-
-
-
-
1
-
1
1
2
-
-
-
1
-
-
-
-
4
1
1
-
-
-
1
1
-
-
-
-
-
-
-
-
693286
Kino
A novel L-amino acid ligase fr ...
Bacillus licheniformis, Bacillus licheniformis NBRC12200
J. Biosci. Bioeng.
106
313-315
2008
-
-
1
-
-
-
-
-
-
1
-
4
-
4
-
-
1
-
-
-
-
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17
-
1
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-
-
1
-
-
1
-
-
-
-
-
1
1
-
-
-
-
-
-
-
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1
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4
-
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1
-
-
-
-
17
-
1
-
-
-
1
-
-
-
-
-
-
-
-
-
671498
Tabata
Fermentative production of L-a ...
Bacillus subtilis
Appl. Environ. Microbiol.
73
6378-6385
2007
-
1
-
-
-
-
-
-
-
-
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2
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1
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662037
Tabata
ywf in Bacillus subtilis codes ...
Bacillus subtilis, Bacillus subtilis 168
J. Bacteriol.
187
5195-5202
2005
-
-
1
-
-
-
2
3
-
2
1
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7
-
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1
-
-
-
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4
1
1
1
-
-
1
1
-
-
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1
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-
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2
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3
-
2
1
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1
-
-
-
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4
1
1
1
-
-
1
1
-
-
-
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-
-
-
-
733219
Steinborn
bac genes for recombinant baci ...
Bacillus amyloliquefaciens, Bacillus amyloliquefaciens ATCC 15841, Bacillus pumilus, Bacillus pumilus ATCC 7065, Bacillus subtilis, Bacillus subtilis 168, Bacillus subtilis A1/3, no activity in Bacillus amyloliquefaciens, no activity in Bacillus amyloliquefaciens GSB272, no activity in Bacillus coagulans, no activity in Bacillus licheniformis, no activity in Bacillus licheniformis ATCC 9789, no activity in Bacillus megaterium, no activity in Bacillus megaterium PV361, no activity in Bacillus pumilus, no activity in Bacillus pumilus ATCC 12140
Arch. Microbiol.
183
71-79
2005
-
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3
-
1
-
-
-
-
3
-
8
-
21
-
-
-
-
-
-
-
-
8
-
-
-
-
-
-
-
-
3
-
-
-
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4
4
-
1
-
-
-
-
-
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4
-
8
-
-
-
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8
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-
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6
7
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