6ZI3

Crystal structure of OleP-6DEB bound to L-rhamnose

Summary for 6ZI3

• Entry DOI: 10.2210/pdb6zi3/pdb
• Related: 6ZHZ 6ZI2
• Descriptor: Cytochrome P-450, PROTOPORPHYRIN IX CONTAINING FE, 6-DEOXYERYTHRONOLIDE B, ... (9 entities in total)
• Functional Keywords: cytochrome p450, 8.8a-deoxyoleandolide monooxygenase, 8.8a-deoxyoleandolide, oxidoreductase
• Biological source: Streptomyces antibioticus
• Total number of polymer chains: 6
• Total formula weight: 287662.57

Authors

Montemiglio, L.C.,Savino, C.,Vallone, B.,Parisi, G.,Freda, I. (deposition date: 2020-06-24, release date: 2020-10-21, Last modification date: 2024-01-31)

Primary citation

Parisi, G.,Freda, I.,Exertier, C.,Cecchetti, C.,Gugole, E.,Cerutti, G.,D'Auria, L.,Macone, A.,Vallone, B.,Savino, C.,Montemiglio, L.C.
Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate.
Biomolecules, 10:-, 2020

PubMed Abstract: The cytochrome P450 OleP catalyzes the epoxidation of aliphatic carbons on both the aglycone 8.8a-deoxyoleandolide (DEO) and the monoglycosylated L-olivosyl-8.8a-deoxyoleandolide (L-O-DEO) intermediates of oleandomycin biosynthesis. We investigated the substrate versatility of the enzyme. X-ray and equilibrium binding data show that the aglycone DEO loosely fits the OleP active site, triggering the closure that prepares it for catalysis only on a minor population of enzyme. The open-to-closed state transition allows solvent molecules to accumulate in a cavity that forms upon closure, mediating protein-substrate interactions. docking of the monoglycosylated L-O-DEO in the closed OleP-DEO structure shows that the L-olivosyl moiety can be hosted in the same cavity, replacing solvent molecules and directly contacting structural elements involved in the transition. X-ray structures of aglycone-bound OleP in the presence of L-rhamnose confirm the cavity as a potential site for sugar binding. All considered, we propose L-O-DEO as the optimal substrate of OleP, the L-olivosyl moiety possibly representing the molecular wedge that triggers a more efficient structural response upon substrate binding, favoring and stabilizing the enzyme closure before catalysis. OleP substrate versatility is supported by structural solvent molecules that compensate for the absence of a glycosyl unit when the aglycone is bound.

PubMed: 33036250
DOI: 10.3390/biom10101411

Experimental method

X-RAY DIFFRACTION (2.08 Å)