2QZZ

Structure of Eugenol Synthase from Ocimum basilicum

DOI: 10.2210/pdb2QZZ/pdb

Classification: PLANT PROTEIN
Organism(s): Ocimum basilicum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-08-17 Released: 2008-01-15
Deposition Author(s): Louie, G.V., Noel, J.P., Bowman, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.287
R-Value Work: 0.259

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure and reaction mechanism of basil eugenol synthase

Louie, G.V., Baiga, T.J., Bowman, M.E., Koeduka, T., Taylor, J.H., Spassova, S.M., Pichersky, E., Noel, J.P.

(2007) PLoS One 2: e993-e993

PubMed: 17912370 Search on PubMedSearch on PubMed Central
DOI: 10.1371/journal.pone.0000993
Primary Citation of Related Structures:
2R2G, 2R6J, 2QX7, 2QW8, 2QYS, 2QZZ

PubMed Abstract:

Phenylpropenes, a large group of plant volatile compounds that serve in multiple roles in defense and pollinator attraction, contain a propenyl side chain. Eugenol synthase (EGS) catalyzes the reductive displacement of acetate from the propenyl side chain of the substrate coniferyl acetate to produce the allyl-phenylpropene eugenol. We report here the structure determination of EGS from basil (Ocimum basilicum) by protein x-ray crystallography. EGS is structurally related to the short-chain dehydrogenase/reductases (SDRs), and in particular, enzymes in the isoflavone-reductase-like subfamily. The structure of a ternary complex of EGS bound to the cofactor NADP(H) and a mixed competitive inhibitor EMDF ((7S,8S)-ethyl (7,8-methylene)-dihydroferulate) provides a detailed view of the binding interactions within the EGS active site and a starting point for mutagenic examination of the unusual reductive mechanism of EGS. The key interactions between EMDF and the EGS-holoenzyme include stacking of the phenyl ring of EMDF against the cofactor's nicotinamide ring and a water-mediated hydrogen-bonding interaction between the EMDF 4-hydroxy group and the side-chain amino moiety of a conserved lysine residue, Lys132. The C4 carbon of nicotinamide resides immediately adjacent to the site of hydride addition, the C7 carbon of cinnamyl acetate substrates. The inhibitor-bound EGS structure suggests a two-step reaction mechanism involving the formation of a quinone-methide prior to reduction. The formation of this intermediate is promoted by a hydrogen-bonding network that favors deprotonation of the substrate's 4-hydroxyl group and disfavors binding of the acetate moiety, akin to a push-pull catalytic mechanism. Notably, the catalytic involvement in EGS of the conserved Lys132 in preparing the phenolic substrate for quinone methide formation through the proton-relay network appears to be an adaptation of the analogous role in hydrogen bonding played by the equivalent lysine residue in other enzymes of the SDR family.

Organizational Affiliation:

Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California, United States of America.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eugenol synthase 1	A, B	318	Ocimum basilicum	Mutation(s): 0 Gene Names: EGS1 EC: 1.1.1.318
Find proteins for Q15GI4 (Ocimum basilicum) Explore Q15GI4 Go to UniProtKB: Q15GI4
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain E [B] MOL2 format, chain C [A] MOL2 format, chain E [B]	A, B	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Ligand Interaction
EMF Query on EMF Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain F [B] MOL2 format, chain D [A] MOL2 format, chain F [B]	A, B	ethyl (1S,2S)-2-(4-hydroxy-3-methoxyphenyl)cyclopropanecarboxylate C₁₃ H₁₆ O₄ QZLUEKVALMNAEZ-ZJUUUORDSA-N		Ligand Interaction