6ZI3 image
Deposition Date 2020-06-24
Release Date 2020-10-21
Last Version Date 2024-01-31
Entry Detail
PDB ID:
6ZI3
Keywords:
Title:
Crystal structure of OleP-6DEB bound to L-rhamnose
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.08 Å
R-Value Free:
0.22
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome P-450
Gene (Uniprot):oleP
Chain IDs:A, B, C, D, E, F
Chain Length:407
Number of Molecules:6
Biological Source:Streptomyces antibioticus
Primary Citation
Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate.
Biomolecules 10 ? ? (2020)
PMID: 33036250 DOI: 10.3390/biom10101411

Abstact

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. In silico 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.

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