2C7X
Crystal structure of narbomycin-bound cytochrome P450 PikC (CYP107L1)
Summary for 2C7X
| Entry DOI | 10.2210/pdb2c7x/pdb |
| Related | 2BVJ 2C6H 2CA0 2CD8 |
| Descriptor | CYTOCHROME P450 MONOOXYGENASE, PROTOPORPHYRIN IX CONTAINING FE, NARBOMYCIN, ... (4 entities in total) |
| Functional Keywords | cytochrome p450, pikc, narbomycin, macrolide monooxygenase, antibiotic biosynthesis, heme, iron, metal-binding, monooxygenase, oxidoreductase |
| Biological source | STREPTOMYCES VENEZUELAE |
| Total number of polymer chains | 1 |
| Total formula weight | 49394.90 |
| Authors | Sherman, D.H.,Li, S.,Yermalitskaya, L.V.,Kim, Y.,Smith, J.A.,Waterman, M.R.,Podust, L.M. (deposition date: 2005-11-29, release date: 2006-07-03, Last modification date: 2023-12-13) |
| Primary citation | Sherman, D.H.,Li, S.,Yermalitskaya, L.V.,Kim, Y.,Smith, J.A.,Waterman, M.R.,Podust, L.M. The Structural Basis for Substrate Anchoring, Active Site Selectivity, and Product Formation by P450 Pikc from Streptomyces Venezuelae. J.Biol.Chem., 281:26289-, 2006 Cited by PubMed Abstract: The pikromycin (Pik)/methymycin biosynthetic pathway of Streptomyces venezuelae represents a valuable system for dissecting the fundamental mechanisms of modular polyketide biosynthesis, aminodeoxysugar assembly, glycosyltransfer, and hydroxylation leading to the production of a series of macrolide antibiotics, including the natural ketolides narbomycin and pikromycin. In this study, we describe four x-ray crystal structures and allied functional studies for PikC, the remarkable P450 monooxygenase responsible for production of a number of related macrolide products from the Pik pathway. The results provide important new insights into the structural basis for the C10/C12 and C12/C14 hydroxylation patterns for the 12-(YC-17) and 14-membered ring (narbomycin) macrolides, respectively. This includes two different ligand-free structures in an asymmetric unit (resolution 2.1 A) and two co-crystal structures with bound endogenous substrates YC-17 (resolution 2.35 A)or narbomycin (resolution 1.7 A). A central feature of the enzyme-substrate interaction involves anchoring of the desosamine residue in two alternative binding pockets based on a series of distinct amino acid residues that form a salt bridge and a hydrogen-bonding network with the deoxysugar C3' dimethylamino group. Functional significance of the salt bridge was corroborated by site-directed mutagenesis that revealed a key role for Glu-94 in YC-17 binding and Glu-85 for narbomycin binding. Taken together, the x-ray structure analysis, site-directed mutagenesis, and corresponding product distribution studies reveal that PikC substrate tolerance and product diversity result from a combination of alternative anchoring modes rather than an induced fit mechanism. PubMed: 16825192DOI: 10.1074/JBC.M605478200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.75 Å) |
Structure validation
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