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Literature summary for 6.3.2.4 extracted from
- Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori (2008), Proteins, 72, 1148-1160.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| expression of N-terminally His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) | Helicobacter pylori |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| recombinant enzyme, 4-8 mg/ml protien in 20 mM Tris-HCl, pH 8.0, 300 mM NaCl, 2 mM MgCl2, hanging drop vapour diffusion method, 4°C, versus a reservoir solution containing 0.1M HEPES, pH 7.5, 10% PEG 6000, 5% MPD, 4 months, X-ray diffraction structure determination and analysisat 2.4 A resolution, molecular replacement | Helicobacter pylori |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| I16V | site-directed mutagenesis of an active site mutant, mutant kinetics compared to the wild-type structure | Helicobacter pylori |
| L241F | site-directed mutagenesis of an active site mutant, mutant kinetics compared to the wild-type structure | Helicobacter pylori |
| L241Y | site-directed mutagenesis of an active site mutant, mutant kinetics compared to the wild-type structure | Helicobacter pylori |
| L308T | site-directed mutagenesis of an active site mutant, mutant kinetics compared to the wild-type structure | Helicobacter pylori |
| Y311S | site-directed mutagenesis of an active site mutant, mutant kinetics compared to the wild-type structure | Helicobacter pylori |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | kinetics of wild-type and mutant enzymes | Helicobacter pylori | |
| 0.00087 | - |
ATP | pH 8.0, 30°C | Helicobacter pylori |  |
| 0.00242 | - |
ATP | pH 9.0, 30°C | Helicobacter pylori | |
| 1.49 | - |
D-alanine | pH 9.0, 30°C | Helicobacter pylori | |
| 1.89 | - |
D-alanine | pH 8.0, 30°C | Helicobacter pylori | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | - |
Helicobacter pylori | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + D-alanine | Helicobacter pylori | - |
ADP + phosphate + D-alanyl-D-alanine | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Helicobacter pylori | Q2N4T5 | strains SS1, 26,695 and J99 | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) | Helicobacter pylori |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + D-alanine | - |
Helicobacter pylori | ADP + phosphate + D-alanyl-D-alanine | - |
? | |
| ATP + D-alanine | the enzyme shows relatively weak binding affinity and poor catalytic activity against the substrate D-Ala in vitro, active site structure, overview | Helicobacter pylori | ADP + phosphate + D-alanyl-D-alanine | - |
? | |
| additional information | no activity with D-Ser, Gly, and D-lactate | Helicobacter pylori | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| dimer | - |
Helicobacter pylori |
| More | 3_10-helix, including residues from Gly306 to Leu312, near the D-Ala binding region in the C-terminal domain probably participates in D-Ala binding and conformational change of the enzyme | Helicobacter pylori |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| Ddl | - |
Helicobacter pylori |
| More | the enzyme is a member of the D-Ala-D-X ligase superfamily | Helicobacter pylori |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 50 | - |
- |
Helicobacter pylori |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 1.9 | - |
ATP | pH 8.0-9.0, 30°C | Helicobacter pylori | |
| 1.9 | - |
D-alanine | pH 8.0-9.0, 30°C | Helicobacter pylori | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 9 | - |
above | Helicobacter pylori |
pH Range
| pH Minimum | pH Maximum | Comment | Organism |
|---|---|---|---|
| additional information | - |
pH profile | Helicobacter pylori |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| ATP | - |
Helicobacter pylori | |
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