EC Number   |
|---|
    6.3.2.4 | - |
| 6.3.2.4 | apo, ADP-bound, ATP-bound, and AMPPNP-bound enzyme, sitting drop vapor diffusion method, mixing of 0.0025 ml of protein solution with 00.0025 ml of reservoir solution containing 15% w/v PEG 4000, 0.1 M Tris, pH 8.5, and 0.2 M MgCl2 with 0.3 M dimethylethyl-(3-sulfopropyl)-ammonium, 14°C, 24 h, ligand-bound enzyme structures by soaking apoenzyme crystals in each nucleotide-containing reservoir solution, X-ray diffraction structure determination and analysis at 2.0-2.3 A resolution, molecular replacement |
| 6.3.2.4 | co-crystallized with an S,R-methylphosphinate and adenosine triphosphate, at 2.3 A resolution |
| 6.3.2.4 | complexed with a D-Ala-D-2-hydroxybutanoate phosphonate, and Y216F mutant ligase complexed with a D-Ala-D-Ala phosphinate, at 2.2A and 1.9A resolution |
| 6.3.2.4 | crystal structure of Staphylococcus aureus D-alanine:D-alanine ligase and its cocrystal structures with 3-chloro-2,2-dimethyl-N-4(trifluoromethyl)phenylpropanamide and with ADP at resolutions of 2.0 A, 2.2 A, and 2.6 A, respectively |
| 6.3.2.4 | hanging-drop vapor-diffusion method, structure of the enzyme is determined in the absence of substrates (open conformation) |
| 6.3.2.4 | in ternary complex with ADP and D-alanyl-D-alanine, to 1.4 A resolution, and with the ligands ATP and D-alanyl-D-alanine, representing the product-inhibited complex, to 1.5 A resolution |
| 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 |
| 6.3.2.4 | purified enzyme in apoform, AMP-bound, ADP-bound, adenosine 5'-(beta,gamma-imido)triphosphate-bound, and D-alanyl-D-alanine, and ADP-bound structures, hanging drop vapour diffusion method, mixing of 900 nl of 8 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 20 mM NaCl, and 3 mM 2-mercaptoethanol, with 900 nl of reservoir solution containing 0.2 M sodium acetate, 0.1 M Bis-Tris, pH 7.0, and 29% PEG 8000, and equilibration against 1 ml of reservoir solution, 14°C, 2 days, method optimization, X-ray diffraction structure determination and analysis 1.7-2.5 A resolution, molecular replacement of the apoenzyme structure using a structure as model, PDB entry 3v4z |
| 6.3.2.4 | purified recombinant enzyme, development of several different crystallization conditions for the AbDDL protein, e.g. sitting drop vapor diffusion method, 14°C, by mixing of 0.06 M MgCl2 and CaCl2, 0.1 M imidazole, 2-(N-morpholino)ethanesulfonic acid-HCl, pH 6.5, with 30% of the precipitant EDO-P8K containing 40% v/v ethylene glycol and 20% w/v PEG 8000, or by microbatch method with 0.2 M NaSCN and 20% w/v PEG 3350 as crystallization solution, X-ray diffraciton structure determination and analysis at 2.2 A resolution, molecular replacement wit the DDL crystal structure from Yestis pestis as a template, PDB ID 3v4z |
