Crystallization (Comment) | Organism |
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structures of the PikC D50N mutant cocrystallized with narbomycin, to 1.85 A resolution, and with 10-deoxymethymycin, to 3.2 A resolution. In the mutant D50N, the desosamine moiety of both 10-deoxymethymycin and narbomycin is bound in a catalytically productive buried site, suggesting a two-step substrate binding mechanism, whereby desosamine is recognized in the two subsites to allow the macrolide substrate to sequentially progress toward a catalytically favorable orientation | Streptomyces venezuelae |
Protein Variants | Comment | Organism |
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D50N | increase in catalytic activity. Binding affinity for 10-desoxymethymycin increases about 4fold, binding affinity for narbomycin about 1.3fold compared to wild-type. 60% conversion of 10-desoxymethymycin, ratio of products neomethymycin to methymycin is 1.15. 44.4% conversion of substrate narbomycin | Streptomyces venezuelae |
D50N/E85Q | 18.4% conversion of 10-desoxymethymycin, ratio of products neomethymycin to methymycin is 0.38. 3.5% conversion of substrate narbomycin | Streptomyces venezuelae |
D50N/E94Q | no conversion of 10-desoxymethymycin. 5.3% conversion of substrate narbomycin | Streptomyces venezuelae |
E85Q | 18% conversion of 10-desoxymethymycin, ratio of products neomethymycin to methymycin is 0.26. 8.1% conversion of substrate narbomycin | Streptomyces venezuelae |
E94Q | no conversion of 10-desoxymethymycin. 5.4% conversion of substrate narbomycin | Streptomyces venezuelae |
Organism | UniProt | Comment | Textmining |
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Streptomyces venezuelae | O87605 | - |
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Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
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10-deoxymethymycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 | i.e. YC-17. 40% conversion, ratio of products neomethymycin to methymycin is 0.81 | Streptomyces venezuelae | methymycin + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O | - |
? | |
10-deoxymethymycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 | 40% conversion, ratio of products neomethymycin to methymycin is 0.81 | Streptomyces venezuelae | neomethymycin + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O | - |
? | |
narbomycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 | binding kinetics are biphasic and accurately described by a double exponential function revealing a fast first phase followed by a slow second one. The kinetic rate of the first binding step, accounting for about 50% of the reaction amplitude, is fast and protein-dependent. The rate of the second step is slow, about 13 per s | Streptomyces venezuelae | pikromycin + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O | 35% conversion | ? |