2C6H

Crystal structure of YC-17-bound cytochrome P450 PikC (CYP107L1)

Summary for 2C6H

• Entry DOI: 10.2210/pdb2c6h/pdb
• Related: 2BVJ 2C7X 2CA0 2CD8
• Descriptor: CYTOCHROME P450 MONOOXYGENASE, PROTOPORPHYRIN IX CONTAINING FE, 4-{[4-(DIMETHYLAMINO)-3-HYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-12-ETHYL-3,5,7,11-TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE, ... (5 entities in total)
• Functional Keywords: oxidoreductase, cytochrome p450, pikc, cyp107l1, macrolide monooxygenase, antibiotic biosynthesis, heme, iron, metal-binding, monooxygenase, oxidoreductase antibiotic biosynthesis
• Biological source: STREPTOMYCES VENEZUELAE
• Total number of polymer chains: 2
• Total formula weight: 99158.00

Authors

Sherman, D.H.,Li, S.,Yermalitskaya, L.V.,Kim, Y.,Smith, J.A.,Waterman, M.R.,Podust, L.M. (deposition date: 2005-11-09, 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

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: 16825192
DOI: 10.1074/JBC.M605478200

Experimental method

X-RAY DIFFRACTION (2.35 Å)