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Literature summary 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.
Crystallization (Commentary)
| EC Number | Crystallization (Comment) | Organism |
|---|---|---|
| 6.3.2.4 | molecular docking study on the orientations of substrates. Residue Arg301 has a dual function in a sequential reaction mechanism, i.e. substrate orientation in subsite 2 as well as stabilization of the transition state. 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-Ala adopts an orientation that utilizes H-bonding to water 2882 and the D-Ala 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-Ala phosphate intermediate for formation of the transition state | Leuconostoc mesenteroides |
Inhibitors
| EC Number | Inhibitors | Comment | Organism | Structure |
|---|---|---|---|---|
| 6.1.2.1 | Vancomycin | - |
Leuconostoc mesenteroides |  |
Metals/Ions
| EC Number | Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|---|
| 6.1.2.1 | Mg2+ | - |
Leuconostoc mesenteroides | |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 6.1.2.1 | 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
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 6.1.2.1 | Leuconostoc mesenteroides | - |
- |
- |
| 6.3.2.4 | Leuconostoc mesenteroides | - |
- |
- |
Reaction
| EC Number | Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|---|
| 6.1.2.1 | 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)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 6.1.2.1 | 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 | ? | - |
? | |
| 6.3.2.4 | ATP + 2 D-Ala | - |
Leuconostoc mesenteroides | ADP + phosphate + D-Ala-D-Ala | - |
? | |
| 6.3.2.4 | ATP + D-Ala + D-lactate | - |
Leuconostoc mesenteroides | ADP + phosphate + D-Ala-D-lactate | depsipeptide D-Ala-D-lactate is responsible for the intrinsic resistance of Leuconostoc mesenteroides to vancomycin | ? | |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 6.1.2.1 | D-alanine:D-alanine (D-lactate) ligase (ADP) | - |
Leuconostoc mesenteroides |
| 6.1.2.1 | D-alanine:D-lactate ligase | - |
Leuconostoc mesenteroides |
Cofactor
| EC Number | Cofactor | Comment | Organism | Structure |
|---|---|---|---|---|
| 6.1.2.1 | ATP | - |
Leuconostoc mesenteroides | |
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