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Literature summary for 6.1.2.1 extracted from
- Role of Arg301 in substrate orientation and catalysis in subsite 2 of D-alanine:D-alanine (D-lactate) ligase from Leuconostoc mesenteroides: A molecular docking study (2010), J. Mol. Graph. Model., 28, 728-734.
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| Vancomycin | - |
Leuconostoc mesenteroides |  |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | - |
Leuconostoc mesenteroides | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | Leuconostoc mesenteroides | D-alanine:D-alanine (D-lactate) ligase (ADP) from Leuconostoc mesenteroides synthesizes the depsipeptide, D-alanyl-D-lactate, in addition to D-alanyl-D-alanine, when D-alanine and D-lactate are incubated simultaneously. Structure of bound D-alanine and D-lactate at the active subsites and substrate orientations, overview. With D-lactate a bifurcated H-bond from Arg301 to the R-OH of D-lactate may account for its orientation and nucleophile activation. This orientation is observed when the guanidino side chain of this residue is flexible. D-Alanine adopts an orientation that utilizes H-bonding to water 2882 and the D-alanyl phosphate in subsite 1. Both of these orientations provide mechanisms of deprotonation and place the nucleophile within 3.2 A of the electrophilic carbonyl of the D-alanyl phosphate intermediate for formation of the transition state, molecular docking and chiral specificity of lactate and alanine dockings, detailed overview | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Leuconostoc mesenteroides | - |
- |
- |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| D-alanine + (R)-lactate + ATP = D-alanyl-(R)-lactate + ADP + phosphate | Arg301 has a dual function in a sequential reaction mechanism, i.e. substrate orientation in subsite 2 aswell as stabilization of the transition state, overview | Leuconostoc mesenteroides |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | D-alanine:D-alanine (D-lactate) ligase (ADP) from Leuconostoc mesenteroides synthesizes the depsipeptide, D-alanyl-D-lactate, in addition to D-alanyl-D-alanine, when D-alanine and D-lactate are incubated simultaneously. Structure of bound D-alanine and D-lactate at the active subsites and substrate orientations, overview. With D-lactate a bifurcated H-bond from Arg301 to the R-OH of D-lactate may account for its orientation and nucleophile activation. This orientation is observed when the guanidino side chain of this residue is flexible. D-Alanine adopts an orientation that utilizes H-bonding to water 2882 and the D-alanyl phosphate in subsite 1. Both of these orientations provide mechanisms of deprotonation and place the nucleophile within 3.2 A of the electrophilic carbonyl of the D-alanyl phosphate intermediate for formation of the transition state, molecular docking and chiral specificity of lactate and alanine dockings, detailed overview | Leuconostoc mesenteroides | ? | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| D-alanine:D-alanine (D-lactate) ligase (ADP) | - |
Leuconostoc mesenteroides |
| D-alanine:D-lactate ligase | - |
Leuconostoc mesenteroides |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| ATP | - |
Leuconostoc mesenteroides | |
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